{bio}[GCCcore/12.3.0,foss/2023a] scNanoGPS v1.1, LIQA v1.3.4, lifelines v0.28.0, ... w/ Perl 5.36.1 #22033

pavelToman · 2024-12-16T11:59:21Z

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#467
needs manual download of annovar sources

…a.eb, lifelines-0.28.0-gfbf-2023a.eb, annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb, BCFtools-1.21-GCC-12.3.0.eb, tabix-0.2.6-GCCcore-12.3.0.eb

github-actions · 2024-12-16T11:59:59Z

Updated software `annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb`

Diff against annovar-20200607-GCCcore-11.2.0-Perl-5.34.0.eb

easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-11.2.0-Perl-5.34.0.eb

diff --git a/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-11.2.0-Perl-5.34.0.eb b/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb
index 36f2f721a0..55490da3de 100644
--- a/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-11.2.0-Perl-5.34.0.eb
+++ b/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb
@@ -11,7 +11,7 @@ description = """ANNOVAR is an efficient software tool to utilize update-to-date
 to functionally annotate genetic variants detected from diverse genomes (including human 
 genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others)."""
 
-toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 # Registration required for download
 # http://www.openbioinformatics.org/annovar/annovar_download_form.php
@@ -19,11 +19,9 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
 sources = ['%(name)s-%(version)s.tar.gz']
 checksums = ['4061af3f2cc8f3d4d8187986c3d468a4b6ae145eec1858e85c7cd1059debb8ed']
 
-dependencies = [('Perl', '5.34.0')]
+dependencies = [('Perl', '5.36.1')]
 
-modextrapaths = {
-    'PATH': '',
-}
+modextrapaths = {'PATH': ''}
 
 sanity_check_paths = {
     'files': ["annotate_variation.pl", "coding_change.pl", "convert2annovar.pl", "retrieve_seq_from_fasta.pl",

Diff against annovar-20191024-GCCcore-8.2.0-Perl-5.28.1.eb

easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-8.2.0-Perl-5.28.1.eb

diff --git a/easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-8.2.0-Perl-5.28.1.eb b/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb
index 67616ff591..55490da3de 100644
--- a/easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-8.2.0-Perl-5.28.1.eb
+++ b/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb
@@ -1,27 +1,27 @@
+# J. Sassmannshausen /NHS/GSTT: toolchain updated to GCCcore-11.2
+
 easyblock = 'Tarball'
 
 name = 'annovar'
-version = '20191024'  # version reported by `annotate_variation.pl -h`
+version = '20200607'  # version reported by `annotate_variation.pl -h`
 versionsuffix = '-Perl-%(perlver)s'
 
 homepage = 'http://annovar.openbioinformatics.org/en/latest/'
-description = """ANNOVAR is an efficient software tool to utilize update-to-date information
-to functionally annotate genetic variants detected from diverse genomes (including human
+description = """ANNOVAR is an efficient software tool to utilize update-to-date information 
+to functionally annotate genetic variants detected from diverse genomes (including human 
 genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others)."""
 
-toolchain = {'name': 'GCCcore', 'version': '8.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 # Registration required for download
 # http://www.openbioinformatics.org/annovar/annovar_download_form.php
 # rename after download to %(name)s-%(version)s.tar.gz
 sources = ['%(name)s-%(version)s.tar.gz']
-checksums = ['78a362a3bd771e4ac46b280c6b52f0d8452f32f11e3812f5d7f85797d26ae799']
+checksums = ['4061af3f2cc8f3d4d8187986c3d468a4b6ae145eec1858e85c7cd1059debb8ed']
 
-dependencies = [('Perl', '5.28.1')]
+dependencies = [('Perl', '5.36.1')]
 
-modextrapaths = {
-    'PATH': '',
-}
+modextrapaths = {'PATH': ''}
 
 sanity_check_paths = {
     'files': ["annotate_variation.pl", "coding_change.pl", "convert2annovar.pl", "retrieve_seq_from_fasta.pl",

Diff against annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb

easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb

diff --git a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb
index 92edb6bb67..55490da3de 100644
--- a/easybuild/easyconfigs/a/annovar/annovar-2016Feb01-foss-2016a-Perl-5.22.1.eb
+++ b/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb
@@ -1,37 +1,37 @@
-# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
-# Modified by Adam Huffman
-# The Francis Crick Institute
+# J. Sassmannshausen /NHS/GSTT: toolchain updated to GCCcore-11.2
 
 easyblock = 'Tarball'
 
 name = 'annovar'
-# Unconventional version is taken from the upstream site
-# http://annovar.openbioinformatics.org/en/latest/user-guide/download/
-version = '2016Feb01'
+version = '20200607'  # version reported by `annotate_variation.pl -h`
 versionsuffix = '-Perl-%(perlver)s'
 
 homepage = 'http://annovar.openbioinformatics.org/en/latest/'
-description = """ ANNOVAR is an efficient software tool to utilize update-to-date information 
- to functionally annotate genetic variants detected from diverse genomes (including human 
- genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others)."""
+description = """ANNOVAR is an efficient software tool to utilize update-to-date information 
+to functionally annotate genetic variants detected from diverse genomes (including human 
+genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others)."""
 
-toolchain = {'name': 'foss', 'version': '2016a'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 # Registration required for download
 # http://www.openbioinformatics.org/annovar/annovar_download_form.php
 # rename after download to %(name)s-%(version)s.tar.gz
 sources = ['%(name)s-%(version)s.tar.gz']
-checksums = ['2b26e514c54a847bfdcf4ce57e43f95c']
+checksums = ['4061af3f2cc8f3d4d8187986c3d468a4b6ae145eec1858e85c7cd1059debb8ed']
 
-dependencies = [('Perl', '5.22.1')]
+dependencies = [('Perl', '5.36.1')]
 
-modextrapaths = {
-    'PATH': '',
-}
+modextrapaths = {'PATH': ''}
 
 sanity_check_paths = {
-    'files': ["annotate_variation.pl", "retrieve_seq_from_fasta.pl"],
+    'files': ["annotate_variation.pl", "coding_change.pl", "convert2annovar.pl", "retrieve_seq_from_fasta.pl",
+              "variants_reduction.pl", "table_annovar.pl"],
     'dirs': ["example", "humandb"],
 }
 
+sanity_check_commands = [
+    "annotate_variation.pl --help 2>&1 | grep 'Version: $Date: %s-%s-%s'" % (version[:4], version[4:6], version[6:]),
+    'retrieve_seq_from_fasta.pl --help 2>&1 | grep "reformat sequences at specific genomic positions"',
+]
+
 moduleclass = 'bio'

Updated software `lifelines-0.28.0-gfbf-2023a.eb`

Diff against lifelines-0.27.4-foss-2022a.eb

easybuild/easyconfigs/l/lifelines/lifelines-0.27.4-foss-2022a.eb

diff --git a/easybuild/easyconfigs/l/lifelines/lifelines-0.27.4-foss-2022a.eb b/easybuild/easyconfigs/l/lifelines/lifelines-0.28.0-gfbf-2023a.eb
index c300ce4d3a..15c494664b 100644
--- a/easybuild/easyconfigs/l/lifelines/lifelines-0.27.4-foss-2022a.eb
+++ b/easybuild/easyconfigs/l/lifelines/lifelines-0.28.0-gfbf-2023a.eb
@@ -1,43 +1,42 @@
 easyblock = 'PythonBundle'
 
 name = 'lifelines'
-version = '0.27.4'
+version = '0.28.0'
 
 homepage = "https://lifelines.readthedocs.io/en/latest/"
-description = """lifelines is a complete survival analysis library, written in pure Python."""
+description = """Lifelines is a complete survival analysis library, written in pure Python."""
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'gfbf', 'version': '2023a'}
 
+builddependencies = [('poetry', '1.5.1')]
 dependencies = [
-    ('Python', '3.10.4'),
-    ('SciPy-bundle', '2022.05'),
-    ('matplotlib', '3.5.2'),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('wrapt', '1.15.0'),
 ]
 
-sanity_pip_check = True
 use_pip = True
+sanity_pip_check = True
 
 exts_list = [
-    ('wrapt', '1.14.1', {
-        'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'],
-    }),
     ('astor', '0.8.1', {
         'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'],
     }),
     ('interface_meta', '1.3.0', {
         'checksums': ['8a4493f8bdb73fb9655dcd5115bc897e207319e36c8835f39c516a2d7e9d79a1'],
     }),
-    ('autograd', '1.5', {
-        'checksums': ['d80bd225154d1db13cb4eaccf7a18c358be72092641b68717f96fcf1d16acd0b'],
+    ('autograd', '1.6.2', {
+        'checksums': ['8731e08a0c4e389d8695a40072ada4512641c113b6cace8f4cfbe8eb7e9aedeb'],
     }),
     ('autograd-gamma', '0.5.0', {
         'checksums': ['f27abb7b8bb9cffc8badcbf59f3fe44a9db39e124ecacf1992b6d952934ac9c4'],
     }),
-    ('formulaic', '0.4.0', {
-        'checksums': ['087950518c53a2491deb52b8ddd66833f953882e517a42e476c007cc8f6892c5'],
+    ('formulaic', '1.0.1', {
+        'checksums': ['64dd7992a7aa5bbceb1e40679d0f01fc6f0ba12b7d23d78094a88c2edc68fba1'],
     }),
     (name, version, {
-        'checksums': ['62f7e911a64c8f723eef4207174fb1df39a94f79eca557cdf53d310eb6be132f'],
+        'checksums': ['eecf726453fd409c94fef8a521f8e593bcd09337f920fe885131f01cfe58b25e'],
     }),
 ]

Diff against lifelines-0.26.3-fosscuda-2020b.eb

easybuild/easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb

diff --git a/easybuild/easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb b/easybuild/easyconfigs/l/lifelines/lifelines-0.28.0-gfbf-2023a.eb
index 2458724db7..15c494664b 100644
--- a/easybuild/easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb
+++ b/easybuild/easyconfigs/l/lifelines/lifelines-0.28.0-gfbf-2023a.eb
@@ -1,44 +1,42 @@
-# This easyconfig was created by the BEAR Software team at the University of Birmingham.
 easyblock = 'PythonBundle'
 
 name = 'lifelines'
-version = '0.26.3'
+version = '0.28.0'
 
 homepage = "https://lifelines.readthedocs.io/en/latest/"
-description = """lifelines is a complete survival analysis library, written in pure Python."""
+description = """Lifelines is a complete survival analysis library, written in pure Python."""
 
-toolchain = {'name': 'fosscuda', 'version': '2020b'}
+toolchain = {'name': 'gfbf', 'version': '2023a'}
 
+builddependencies = [('poetry', '1.5.1')]
 dependencies = [
-    ('Python', '3.8.6'),
-    ('SciPy-bundle', '2020.11'),
-    ('matplotlib', '3.3.3'),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('wrapt', '1.15.0'),
 ]
 
-sanity_pip_check = True
 use_pip = True
+sanity_pip_check = True
 
 exts_list = [
-    ('wrapt', '1.12.1', {
-        'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'],
-    }),
     ('astor', '0.8.1', {
         'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'],
     }),
-    ('interface_meta', '1.2.4', {
-        'checksums': ['4c7725dd4b80f97b7eecfb26023e1a8a7cdbb6d6a7207a8e93f9d4bfef9ee566'],
+    ('interface_meta', '1.3.0', {
+        'checksums': ['8a4493f8bdb73fb9655dcd5115bc897e207319e36c8835f39c516a2d7e9d79a1'],
     }),
-    ('autograd', '1.3', {
-        'checksums': ['a15d147577e10de037de3740ca93bfa3b5a7cdfbc34cfb9105429c3580a33ec4'],
+    ('autograd', '1.6.2', {
+        'checksums': ['8731e08a0c4e389d8695a40072ada4512641c113b6cace8f4cfbe8eb7e9aedeb'],
     }),
     ('autograd-gamma', '0.5.0', {
         'checksums': ['f27abb7b8bb9cffc8badcbf59f3fe44a9db39e124ecacf1992b6d952934ac9c4'],
     }),
-    ('formulaic', '0.2.4', {
-        'checksums': ['15b71ea8972fb451f80684203cddd49620fc9ed5c2e35f31e0874e9c41910d1a'],
+    ('formulaic', '1.0.1', {
+        'checksums': ['64dd7992a7aa5bbceb1e40679d0f01fc6f0ba12b7d23d78094a88c2edc68fba1'],
     }),
     (name, version, {
-        'checksums': ['f3dc77601927b9dbebb77d1b4d6f5bd4e5e3e169f6e8d7c2beb31a9a36fcbe1b'],
+        'checksums': ['eecf726453fd409c94fef8a521f8e593bcd09337f920fe885131f01cfe58b25e'],
     }),
 ]

Diff against lifelines-0.22.8-fosscuda-2019a-Python-3.7.2.eb

easybuild/easyconfigs/l/lifelines/lifelines-0.22.8-fosscuda-2019a-Python-3.7.2.eb

diff --git a/easybuild/easyconfigs/l/lifelines/lifelines-0.22.8-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/l/lifelines/lifelines-0.28.0-gfbf-2023a.eb
index 89538a82d5..15c494664b 100644
--- a/easybuild/easyconfigs/l/lifelines/lifelines-0.22.8-fosscuda-2019a-Python-3.7.2.eb
+++ b/easybuild/easyconfigs/l/lifelines/lifelines-0.28.0-gfbf-2023a.eb
@@ -1,44 +1,43 @@
-# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
-
 easyblock = 'PythonBundle'
 
 name = 'lifelines'
-version = '0.22.8'
-versionsuffix = '-Python-%(pyver)s'
+version = '0.28.0'
 
-homepage = 'https://lifelines.readthedocs.io'
-description = """lifelines is a pure Python implementation of the best parts of
-survival analysis"""
+homepage = "https://lifelines.readthedocs.io/en/latest/"
+description = """Lifelines is a complete survival analysis library, written in pure Python."""
 
-toolchain = {'name': 'fosscuda', 'version': '2019a'}
+toolchain = {'name': 'gfbf', 'version': '2023a'}
 
+builddependencies = [('poetry', '1.5.1')]
 dependencies = [
-    ('Python', '3.7.2'),
-    ('matplotlib', '3.0.3', versionsuffix),
-    ('SciPy-bundle', '2019.03'),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('matplotlib', '3.7.2'),
+    ('wrapt', '1.15.0'),
 ]
 
 use_pip = True
+sanity_pip_check = True
 
 exts_list = [
-    ('autograd', '1.3', {
-        'checksums': ['a15d147577e10de037de3740ca93bfa3b5a7cdfbc34cfb9105429c3580a33ec4'],
+    ('astor', '0.8.1', {
+        'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'],
+    }),
+    ('interface_meta', '1.3.0', {
+        'checksums': ['8a4493f8bdb73fb9655dcd5115bc897e207319e36c8835f39c516a2d7e9d79a1'],
+    }),
+    ('autograd', '1.6.2', {
+        'checksums': ['8731e08a0c4e389d8695a40072ada4512641c113b6cace8f4cfbe8eb7e9aedeb'],
     }),
-    ('autograd-gamma', '0.4.1', {
-        'checksums': ['3b4349cb415bd6e28dd2fac5055e34de1b6c87fe711757a0e42a84bd650fba35'],
+    ('autograd-gamma', '0.5.0', {
+        'checksums': ['f27abb7b8bb9cffc8badcbf59f3fe44a9db39e124ecacf1992b6d952934ac9c4'],
+    }),
+    ('formulaic', '1.0.1', {
+        'checksums': ['64dd7992a7aa5bbceb1e40679d0f01fc6f0ba12b7d23d78094a88c2edc68fba1'],
     }),
     (name, version, {
-        'source_tmpl': 'v%(version)s.tar.gz',
-        'source_urls': ['https://github.com/CamDavidsonPilon/lifelines/archive/'],
-        'checksums': ['637eefb86abe0d7b5952c3872bae86ee22cd8adfa2a27e4b3015bf994c799d67'],
+        'checksums': ['eecf726453fd409c94fef8a521f8e593bcd09337f920fe885131f01cfe58b25e'],
     }),
 ]
 
-sanity_check_paths = {
-    'files': [],
-    'dirs': ['lib/python%(pyshortver)s/site-packages/autograd',
-             'lib/python%(pyshortver)s/site-packages/autograd_gamma',
-             'lib/python%(pyshortver)s/site-packages/lifelines'],
-}
-
 moduleclass = 'bio'

Updated software `tabix-0.2.6-GCCcore-12.3.0.eb`

Diff against tabix-0.2.6-GCCcore-11.3.0.eb

easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-12.3.0.eb
index 7b219ea3fb..c27a6c1f60 100644
--- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-12.3.0.eb
@@ -16,15 +16,15 @@ version = '0.2.6'
 homepage = 'https://samtools.sourceforge.net'
 description = """ Generic indexer for TAB-delimited genome position files """
 
-toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 source_urls = [('https://sourceforge.net/projects/samtools/files/', 'download')]
 sources = [SOURCE_TAR_BZ2]
 checksums = ['e4066be7101bae83bec62bc2bc6917013f6c2875b66eb5055fbb013488d68b73']
 
-builddependencies = [('binutils', '2.38')]
+builddependencies = [('binutils', '2.40')]
 
-dependencies = [('zlib', '1.2.12')]
+dependencies = [('zlib', '1.2.13')]
 
 buildopts = 'CC="$CC" CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"'

Diff against tabix-0.2.6-GCCcore-10.3.0.eb

easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-10.3.0.eb

diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-12.3.0.eb
index ab99f4cfb2..c27a6c1f60 100644
--- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-10.3.0.eb
+++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-12.3.0.eb
@@ -13,24 +13,26 @@ easyblock = 'MakeCp'
 name = 'tabix'
 version = '0.2.6'
 
-homepage = 'http://samtools.sourceforge.net'
+homepage = 'https://samtools.sourceforge.net'
 description = """ Generic indexer for TAB-delimited genome position files """
 
-toolchain = {'name': 'GCCcore', 'version': '10.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 source_urls = [('https://sourceforge.net/projects/samtools/files/', 'download')]
 sources = [SOURCE_TAR_BZ2]
 checksums = ['e4066be7101bae83bec62bc2bc6917013f6c2875b66eb5055fbb013488d68b73']
 
-builddependencies = [('binutils', '2.36.1')]
+builddependencies = [('binutils', '2.40')]
 
-dependencies = [('zlib', '1.2.11')]
+dependencies = [('zlib', '1.2.13')]
 
 buildopts = 'CC="$CC" CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"'
 
 files_to_copy = [
     (["tabix", "bgzip", "tabix.py"], "bin"),
     (["tabix.1"], "man/man1"),
+    (["libtabix.a"], "lib64"),
+    (["*.h"], "include"),
     "example.gtf.gz",
     "example.gtf.gz.tbi",
     "NEWS",
@@ -38,8 +40,8 @@ files_to_copy = [
 ]
 
 sanity_check_paths = {
-    'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"],
-    'dirs': [""],
+    'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py", "lib/libtabix.a"],
+    'dirs': ["include"],
 }
 
 moduleclass = 'bio'

Diff against tabix-0.2.6-GCCcore-11.2.0.eb

easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-11.2.0.eb

diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-12.3.0.eb
index 3ab83eb29a..c27a6c1f60 100644
--- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-12.3.0.eb
@@ -13,18 +13,18 @@ easyblock = 'MakeCp'
 name = 'tabix'
 version = '0.2.6'
 
-homepage = 'http://samtools.sourceforge.net'
+homepage = 'https://samtools.sourceforge.net'
 description = """ Generic indexer for TAB-delimited genome position files """
 
-toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 source_urls = [('https://sourceforge.net/projects/samtools/files/', 'download')]
 sources = [SOURCE_TAR_BZ2]
 checksums = ['e4066be7101bae83bec62bc2bc6917013f6c2875b66eb5055fbb013488d68b73']
 
-builddependencies = [('binutils', '2.37')]
+builddependencies = [('binutils', '2.40')]
 
-dependencies = [('zlib', '1.2.11')]
+dependencies = [('zlib', '1.2.13')]
 
 buildopts = 'CC="$CC" CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"'

pavelToman · 2024-12-16T12:14:57Z

Test report by @pavelToman
SUCCESS
Build succeeded for 6 out of 6 (6 easyconfigs in total)
node4012.donphan.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 545.23.08, Python 3.6.8
See https://gist.github.com/pavelToman/ac8ff55e832eaac82a53f3a7dd8150f5 for a full test report.

pavelToman · 2024-12-16T12:31:26Z

Test report by @pavelToman
SUCCESS
Build succeeded for 7 out of 7 (6 easyconfigs in total)
node4202.shinx.os - Linux RHEL 9.4, x86_64, AMD EPYC 9654 96-Core Processor, Python 3.9.18
See https://gist.github.com/pavelToman/08505e461b36694afcccc9d64a3a5651 for a full test report.

pavelToman · 2024-12-16T12:43:06Z

Test report by @pavelToman
SUCCESS
Build succeeded for 9 out of 9 (6 easyconfigs in total)
node3900.accelgor.os - Linux RHEL 9.4, x86_64, AMD EPYC 7413 24-Core Processor, Python 3.9.18
See https://gist.github.com/pavelToman/98c99b6854286761576b17faec869a45 for a full test report.

pavelToman · 2024-12-16T15:00:39Z

Test report by @pavelToman
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
node4003.donphan.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 545.23.08, Python 3.6.8
See https://gist.github.com/pavelToman/0a9bf3eca7baa1c20eec9170504a08be for a full test report.

adding easyconfigs: scNanoGPS-1.1-foss-2023a.eb, LIQA-1.3.4-foss-2023…

fe34f60

…a.eb, lifelines-0.28.0-gfbf-2023a.eb, annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb, BCFtools-1.21-GCC-12.3.0.eb, tabix-0.2.6-GCCcore-12.3.0.eb

pavelToman added new update labels Dec 16, 2024

pavelToman mentioned this pull request Dec 16, 2024

scNanoGPS vscentrum/vsc-software-stack#467

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pavelToman and others added 2 commits December 16, 2024 13:54

Update annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb - fix comma

c8b1ab5

update BCFtools dependency

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{bio}[GCCcore/12.3.0,foss/2023a] scNanoGPS v1.1, LIQA v1.3.4, lifelines v0.28.0, ... w/ Perl 5.36.1 #22033

{bio}[GCCcore/12.3.0,foss/2023a] scNanoGPS v1.1, LIQA v1.3.4, lifelines v0.28.0, ... w/ Perl 5.36.1 #22033

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{bio}[GCCcore/12.3.0,foss/2023a] scNanoGPS v1.1, LIQA v1.3.4, lifelines v0.28.0, ... w/ Perl 5.36.1 #22033

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{bio}[GCCcore/12.3.0,foss/2023a] scNanoGPS v1.1, LIQA v1.3.4, lifelines v0.28.0, ... w/ Perl 5.36.1 #22033

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Updated software annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb

Updated software lifelines-0.28.0-gfbf-2023a.eb

Updated software tabix-0.2.6-GCCcore-12.3.0.eb

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Updated software `annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb`

Updated software `lifelines-0.28.0-gfbf-2023a.eb`

Updated software `tabix-0.2.6-GCCcore-12.3.0.eb`