Add easyconfig Bio-DB-HTS-3.01-GCC-13.2.0.eb #21794

julianmorillo · 2024-11-06T15:50:53Z

No description provided.

github-actions · 2024-11-06T15:51:24Z

Updated software `Bio-DB-HTS-3.01-GCC-13.2.0.eb`

Diff against Bio-DB-HTS-3.01-GCC-12.2.0.eb

easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.2.0.eb

diff --git a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.2.0.eb b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-13.2.0.eb
index a3de8e7098..3c730f7cdb 100644
--- a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.2.0.eb
+++ b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-13.2.0.eb
@@ -6,18 +6,18 @@ 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': '12.2.0'}
+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', '1.9.3')]
+builddependencies = [('pkgconf', '2.0.3')]
 
 dependencies = [
-    ('Perl', '5.36.0'),
+    ('Perl', '5.38.0'),
     ('BioPerl', '1.7.8'),
-    ('HTSlib', '1.17'),
+    ('HTSlib', '1.19.1'),
 ]
 
 preconfigopts = "env HTSLIB_DIR=$EBROOTHTSLIB"

Diff against Bio-DB-HTS-3.01-GCC-11.3.0.eb

easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-13.2.0.eb
index 68542cd0da..3c730f7cdb 100644
--- a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.3.0.eb
+++ b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-13.2.0.eb
@@ -6,18 +6,18 @@ 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': '11.3.0'}
+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', '1.8.0')]
+builddependencies = [('pkgconf', '2.0.3')]
 
 dependencies = [
-    ('Perl', '5.34.1'),
+    ('Perl', '5.38.0'),
     ('BioPerl', '1.7.8'),
-    ('HTSlib', '1.15.1'),
+    ('HTSlib', '1.19.1'),
 ]
 
 preconfigopts = "env HTSLIB_DIR=$EBROOTHTSLIB"

Diff against Bio-DB-HTS-3.01-GCC-11.2.0.eb

easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.2.0.eb

diff --git a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-13.2.0.eb
index 87359ee843..3c730f7cdb 100644
--- a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-13.2.0.eb
@@ -6,18 +6,18 @@ 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': '11.2.0'}
+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', '1.8.0')]
+builddependencies = [('pkgconf', '2.0.3')]
 
 dependencies = [
-    ('Perl', '5.34.0'),
+    ('Perl', '5.38.0'),
     ('BioPerl', '1.7.8'),
-    ('HTSlib', '1.14'),
+    ('HTSlib', '1.19.1'),
 ]
 
 preconfigopts = "env HTSLIB_DIR=$EBROOTHTSLIB"

Updated software `BioPerl-1.7.8-GCCcore-13.2.0.eb`

Diff against BioPerl-1.7.8-GCCcore-13.3.0.eb

easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.2.0.eb
index ba3029a6a4..73cecdb978 100644
--- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.2.0.eb
@@ -14,13 +14,13 @@ 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': '13.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
-builddependencies = [('binutils', '2.42')]
+builddependencies = [('binutils', '2.40')]
 
 dependencies = [
-    ('Perl', '5.38.2'),
-    ('Perl-bundle-CPAN', '5.38.2'),
+    ('Perl', '5.38.0'),
+    ('Perl-bundle-CPAN', '5.38.0'),
     ('XML-LibXML', '2.0210'),
     ('DB_File', '1.859'),
 ]

Diff against BioPerl-1.7.8-GCCcore-12.3.0.eb

easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.2.0.eb
index 4212570abb..73cecdb978 100644
--- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.2.0.eb
@@ -14,14 +14,14 @@ 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': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 builddependencies = [('binutils', '2.40')]
 
 dependencies = [
-    ('Perl', '5.36.1'),
-    ('Perl-bundle-CPAN', '5.36.1'),
-    ('XML-LibXML', '2.0209'),
+    ('Perl', '5.38.0'),
+    ('Perl-bundle-CPAN', '5.38.0'),
+    ('XML-LibXML', '2.0210'),
     ('DB_File', '1.859'),
 ]

Diff against BioPerl-1.7.8-GCCcore-12.2.0.eb

easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.2.0.eb
index e8e52099b0..73cecdb978 100644
--- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.2.0.eb
@@ -10,17 +10,19 @@ easyblock = 'Bundle'
 name = 'BioPerl'
 version = '1.7.8'
 
-homepage = 'http://www.bioperl.org/'
+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': '12.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
-builddependencies = [('binutils', '2.39')]
+builddependencies = [('binutils', '2.40')]
 
 dependencies = [
-    ('Perl', '5.36.0'),
-    ('XML-LibXML', '2.0208'),
+    ('Perl', '5.38.0'),
+    ('Perl-bundle-CPAN', '5.38.0'),
+    ('XML-LibXML', '2.0210'),
+    ('DB_File', '1.859'),
 ]
 
 exts_defaultclass = 'PerlModule'

Updated software `DB-18.1.40-GCCcore-13.2.0.eb`

Diff against DB-18.1.40-GCCcore-13.3.0.eb

easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.2.0.eb
index 6402282780..a15e88f596 100644
--- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.2.0.eb
@@ -7,7 +7,7 @@ description = """Berkeley DB enables the development of custom data management
  solutions, without the overhead traditionally associated with such custom
  projects."""
 
-toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 # use http to allow auto-downloading...
 source_urls = ['http://download.oracle.com/berkeley-db/']
@@ -18,9 +18,9 @@ checksums = [
     '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d',  # DB-18.1.40_fix_doc_install.patch
 ]
 
-builddependencies = [('binutils', '2.42')]
+builddependencies = [('binutils', '2.40')]
 
-dependencies = [('OpenSSL', '3', '', SYSTEM)]
+dependencies = [('OpenSSL', '1.1', '', SYSTEM)]
 
 sanity_check_paths = {
     'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup',

Diff against DB-18.1.40-GCCcore-12.3.0.eb

easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.2.0.eb
index 5d02753039..a15e88f596 100644
--- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.2.0.eb
@@ -7,7 +7,7 @@ description = """Berkeley DB enables the development of custom data management
  solutions, without the overhead traditionally associated with such custom
  projects."""
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 # use http to allow auto-downloading...
 source_urls = ['http://download.oracle.com/berkeley-db/']

Diff against DB-18.1.40-GCCcore-12.2.0.eb

easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.2.0.eb
index 83b4de9932..a15e88f596 100644
--- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.2.0.eb
@@ -7,7 +7,7 @@ description = """Berkeley DB enables the development of custom data management
  solutions, without the overhead traditionally associated with such custom
  projects."""
 
-toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 # use http to allow auto-downloading...
 source_urls = ['http://download.oracle.com/berkeley-db/']
@@ -18,7 +18,7 @@ checksums = [
     '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d',  # DB-18.1.40_fix_doc_install.patch
 ]
 
-builddependencies = [('binutils', '2.39')]
+builddependencies = [('binutils', '2.40')]
 
 dependencies = [('OpenSSL', '1.1', '', SYSTEM)]

Updated software `DB_File-1.859-GCCcore-13.2.0.eb`

Diff against DB_File-1.859-GCCcore-13.3.0.eb

easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.3.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.2.0.eb
index e7120c9c13..7e40f6d223 100644
--- a/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.2.0.eb
@@ -6,18 +6,18 @@ version = '1.859'
 homepage = 'https://perldoc.perl.org/DB_File.html'
 description = """Perl5 access to Berkeley DB version 1.x."""
 
-toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+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', '2.42'),
+    ('binutils', '2.40'),
 ]
 
 dependencies = [
-    ('Perl', '5.38.2'),
+    ('Perl', '5.38.0'),
     ('DB', '18.1.40'),
 ]

Diff against DB_File-1.859-GCCcore-12.3.0.eb

easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.2.0.eb
index 0efe26d544..7e40f6d223 100644
--- a/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.2.0.eb
@@ -6,7 +6,7 @@ version = '1.859'
 homepage = 'https://perldoc.perl.org/DB_File.html'
 description = """Perl5 access to Berkeley DB version 1.x."""
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 source_urls = ['https://www.cpan.org/modules/by-module/DB_File/PMQS']
 sources = [SOURCE_TAR_GZ]
@@ -17,7 +17,7 @@ builddependencies = [
 ]
 
 dependencies = [
-    ('Perl', '5.36.1'),
+    ('Perl', '5.38.0'),
     ('DB', '18.1.40'),
 ]

Diff against DB_File-1.858-GCCcore-11.3.0.eb

easybuild/easyconfigs/d/DB_File/DB_File-1.858-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.858-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.2.0.eb
index a9579572f7..7e40f6d223 100644
--- a/easybuild/easyconfigs/d/DB_File/DB_File-1.858-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.2.0.eb
@@ -1,23 +1,23 @@
 easyblock = 'PerlModule'
 
 name = 'DB_File'
-version = '1.858'
+version = '1.859'
 
 homepage = 'https://perldoc.perl.org/DB_File.html'
 description = """Perl5 access to Berkeley DB version 1.x."""
 
-toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 source_urls = ['https://www.cpan.org/modules/by-module/DB_File/PMQS']
 sources = [SOURCE_TAR_GZ]
-checksums = ['ceb7a2868bd71f87b31e8b7c38d6f8cc0a31fb0322a377ee448994f094d0a7f6']
+checksums = ['5674e0d2cd0b060c4d1253670ea022c64d842a55257f9eb8edb19c0f53e2565c']
 
 builddependencies = [
-    ('binutils', '2.38'),
+    ('binutils', '2.40'),
 ]
 
 dependencies = [
-    ('Perl', '5.34.1'),
+    ('Perl', '5.38.0'),
     ('DB', '18.1.40'),
 ]

…ome dependencies

easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.2.0.eb

easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.2.0.eb

easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.2.0.eb

easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-13.2.0.eb

easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.2.0.eb

…-HTS

on Debian systems

…-HTS

Co-authored-by: Mikael Öhman <[email protected]>

…-HTS

Add easyconfig Bio-DB-HTS-3.01-GCC-13.2.0.eb

7a41087

github-actions bot added the update label Nov 6, 2024

julianmorillo added 5 commits November 6, 2024 16:54

Upgrade Perl and HTSlib versions in Bio-DB-HTS-3.01-GCC-13.2.0.eb

6b6d86e

Upgrade pkgconf version in Bio-DB-HTS-3.01-GCC-13.2.0.eb

e013701

Add easyconfig BioPerl-1.7.8-GCCcore-13.2.0.eb

97980df

Add easyconfig d/DB_File/DB_File-1.859-GCCcore-13.2.0.eb and adjust s…

02d8aec

…ome dependencies

Add easyconfig DB-18.1.40-GCCcore-13.2.0.eb

f2791ed

github-actions bot added the change label Nov 6, 2024

Micket requested changes Nov 7, 2024

View reviewed changes

Merge branch 'easybuilders:develop' into easybuild-easyconfigs-Bio-DB…

8ff539c

…-HTS

github-actions bot removed the change label Nov 7, 2024

Disable two tests in Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb that fail

ad8a464

on Debian systems

github-actions bot added the change label Nov 7, 2024

julianmorillo and others added 8 commits November 7, 2024 18:14

Disable a failing test in Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb

6779fdf

Merge branch 'easybuilders:develop' into easybuild-easyconfigs-Bio-DB…

b25db56

…-HTS

Update easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-13.2.0.eb

2474e6f

Co-authored-by: Mikael Öhman <[email protected]>

Update easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.2.0.eb

34c4837

Co-authored-by: Mikael Öhman <[email protected]>

Update easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-13.2.0.eb

513cae5

Co-authored-by: Mikael Öhman <[email protected]>

Update easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-13.2.0.eb

141e957

Co-authored-by: Mikael Öhman <[email protected]>

Update easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-13.2.0.eb

4e40dd4

Co-authored-by: Mikael Öhman <[email protected]>

Merge branch 'easybuilders:develop' into easybuild-easyconfigs-Bio-DB…

a29b6f0

…-HTS

julianmorillo mentioned this pull request Dec 2, 2024

Add easyconfig Bio-SearchIO-hmmer-1.7.3-GCC-13.2.0.eb #21814

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Add easyconfig Bio-DB-HTS-3.01-GCC-13.2.0.eb #21794

Add easyconfig Bio-DB-HTS-3.01-GCC-13.2.0.eb #21794

julianmorillo commented Nov 6, 2024

github-actions bot commented Nov 6, 2024 •

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Add easyconfig Bio-DB-HTS-3.01-GCC-13.2.0.eb #21794

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Add easyconfig Bio-DB-HTS-3.01-GCC-13.2.0.eb #21794

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julianmorillo commented Nov 6, 2024

github-actions bot commented Nov 6, 2024 • edited Loading

Updated software Bio-DB-HTS-3.01-GCC-13.2.0.eb

Updated software BioPerl-1.7.8-GCCcore-13.2.0.eb

Updated software DB-18.1.40-GCCcore-13.2.0.eb

Updated software DB_File-1.859-GCCcore-13.2.0.eb

github-actions bot commented Nov 6, 2024 •

edited

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Updated software `Bio-DB-HTS-3.01-GCC-13.2.0.eb`

Updated software `BioPerl-1.7.8-GCCcore-13.2.0.eb`

Updated software `DB-18.1.40-GCCcore-13.2.0.eb`

Updated software `DB_File-1.859-GCCcore-13.2.0.eb`