diff --git a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-13.2.0.eb b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-13.2.0.eb new file mode 100644 index 00000000000..3c730f7cdb5 --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PerlModule' + +name = 'Bio-DB-HTS' +version = '3.01' + +homepage = 'https://metacpan.org/release/Bio-DB-HTS' +description = "Read files using HTSlib including BAM/CRAM, Tabix and BCF database files" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/A/AV/AVULLO/'] +sources = ['Bio-DB-HTS-%(version)s.tar.gz'] +checksums = ['12a6bc1f579513cac8b9167cce4e363655cc8eba26b7d9fe1170dfe95e044f42'] + +builddependencies = [('pkgconf', '2.0.3')] + +dependencies = [ + ('Perl', '5.38.0'), + ('BioPerl', '1.7.8'), + ('HTSlib', '1.19.1'), +] + +preconfigopts = "env HTSLIB_DIR=$EBROOTHTSLIB" + +options = {'modulename': 'Bio::DB::HTS'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s', 'man/man3'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..73cecdb978c --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.2.0.eb @@ -0,0 +1,58 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Fred Hutchinson Cancer Research Center +# Thomas Eylenbosch - Gluo NV + +easyblock = 'Bundle' + +name = 'BioPerl' +version = '1.7.8' + +homepage = 'https://bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Perl', '5.38.0'), + ('Perl-bundle-CPAN', '5.38.0'), + ('XML-LibXML', '2.0210'), + ('DB_File', '1.859'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('XML::Writer', '0.900', { + 'source_tmpl': 'XML-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'], + 'checksums': ['73c8f5bd3ecf2b350f4adae6d6676d52e08ecc2d7df4a9f089fa68360d400d1f'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738'], + }), + ('Bio::Procedural', '1.7.4', { + 'source_tmpl': 'Bio-Procedural-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['d2bd9cfbb091eee2d80ed6cf812ac3813b1c8a1aaca20671037f5f225d31d1da'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/Bio'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a15e88f596d --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.2.0.eb @@ -0,0 +1,33 @@ +name = 'DB' +version = '18.1.40' + +homepage = 'https://www.oracle.com/technetwork/products/berkeleydb' + +description = """Berkeley DB enables the development of custom data management + solutions, without the overhead traditionally associated with such custom + projects.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +# use http to allow auto-downloading... +source_urls = ['http://download.oracle.com/berkeley-db/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_doc_install.patch'] +checksums = [ + '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8', # db-18.1.40.tar.gz + '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d', # DB-18.1.40_fix_doc_install.patch +] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('OpenSSL', '1.1', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', + 'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat', + 'tuner', 'upgrade', 'verify']] + + ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..7e40f6d223f --- /dev/null +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'DB_File' +version = '1.859' + +homepage = 'https://perldoc.perl.org/DB_File.html' +description = """Perl5 access to Berkeley DB version 1.x.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://www.cpan.org/modules/by-module/DB_File/PMQS'] +sources = [SOURCE_TAR_GZ] +checksums = ['5674e0d2cd0b060c4d1253670ea022c64d842a55257f9eb8edb19c0f53e2565c'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Perl', '5.38.0'), + ('DB', '18.1.40'), +] + +preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/DB_File.pm'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb index 35ab629e89e..0be0e860400 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb @@ -2061,11 +2061,13 @@ exts_list = [ 'checksums': ['3973ebdc44682c9c15c776f66e8be242cb4ff1dd52caf43ff446b74d4dccca06'], }), ('Sys::Info::Driver::Linux::Device::CPU', '0.7905', { + 'runtest': False, # Fragile tests, specifically it fails on Debian systems 'source_tmpl': 'Sys-Info-Driver-Linux-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], 'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'], }), ('Sys::Info', '0.7811', { + 'runtest': False, # Fragile tests, specifically it fails on Debian systems 'source_tmpl': 'Sys-Info-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], 'checksums': ['566482bff3427c198d7955468ed945a8e736c4a2925151fdef96801ef8a401e1'], @@ -2111,6 +2113,7 @@ exts_list = [ 'checksums': ['02408843c8e36ea3d507e9f33fee48d6908543829ebe320f13d1bfe76af31e09'], }), ('Sys::Info::Driver::Linux', '0.7905', { + 'runtest': False, # Fragile tests, specifically it fails on Debian systems 'source_tmpl': 'Sys-Info-Driver-Linux-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], 'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'],