{bio}[GCCcore/12.3.0,foss/2023a] scNanoGPS v1.1, LIQA v1.3.4, lifelines v0.28.0, annovar v20200607, tabix v0.2.6 by pavelToman · Pull Request #22033 · easybuilders/easybuild-easyconfigs

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.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.eb
index 36f2f721a0..c3bf822435 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.eb
@@ -4,26 +4,25 @@ easyblock = 'Tarball'
 
 name = 'annovar'
 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)."""
 
-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
-# rename after download to %(name)s-%(version)s.tar.gz
+download_instructions = """
+Registration required for download
+via 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 = ['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.eb
index 67616ff591..c3bf822435 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.eb
@@ -1,27 +1,28 @@
+# J. Sassmannshausen /NHS/GSTT: toolchain updated to GCCcore-11.2
+
 easyblock = 'Tarball'
 
 name = 'annovar'
-version = '20191024'  # version reported by `annotate_variation.pl -h`
-versionsuffix = '-Perl-%(perlver)s'
+version = '20200607'  # version reported by `annotate_variation.pl -h`
 
 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
+download_instructions = """
+Registration required for download
+via 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.eb
index 92edb6bb67..c3bf822435 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.eb
@@ -1,37 +1,38 @@
-# 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'
-versionsuffix = '-Perl-%(perlver)s'
+version = '20200607'  # version reported by `annotate_variation.pl -h`
 
 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
+download_instructions = """
+Registration required for download
+via 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-0.27.7-foss-2022b.eb

easybuild/easyconfigs/l/lifelines/lifelines-0.27.7-foss-2022b.eb

diff --git a/easybuild/easyconfigs/l/lifelines/lifelines-0.27.7-foss-2022b.eb b/easybuild/easyconfigs/l/lifelines/lifelines-0.28.0-gfbf-2023a.eb
index 69b35bc787..15c494664b 100644
--- a/easybuild/easyconfigs/l/lifelines/lifelines-0.27.7-foss-2022b.eb
+++ b/easybuild/easyconfigs/l/lifelines/lifelines-0.28.0-gfbf-2023a.eb
@@ -1,26 +1,25 @@
 easyblock = 'PythonBundle'
 
 name = 'lifelines'
-version = '0.27.7'
+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': '2022b'}
+toolchain = {'name': 'gfbf', 'version': '2023a'}
 
+builddependencies = [('poetry', '1.5.1')]
 dependencies = [
-    ('Python', '3.10.8'),
-    ('SciPy-bundle', '2023.02'),
-    ('matplotlib', '3.7.0'),
+    ('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 = [
-    ('wrapt', '1.16.0', {
-        'checksums': ['5f370f952971e7d17c7d1ead40e49f32345a7f7a5373571ef44d800d06b1899d'],
-    }),
     ('astor', '0.8.1', {
         'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'],
     }),
@@ -37,8 +36,7 @@ exts_list = [
         'checksums': ['64dd7992a7aa5bbceb1e40679d0f01fc6f0ba12b7d23d78094a88c2edc68fba1'],
     }),
     (name, version, {
-        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
-        'checksums': ['44d60171f5abe85506b55cdf754b4ba769f61a5f8f18a9d05491009c6cee5803'],
+        'checksums': ['eecf726453fd409c94fef8a521f8e593bcd09337f920fe885131f01cfe58b25e'],
     }),
 ]

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'],
     }),
 ]

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.

boegel · 2025-01-08T10:48:37Z

@boegelbot please test @ generoso

boegelbot · 2025-01-08T10:50:06Z

@boegel: Request for testing this PR well received on login1

PR test command 'EB_PR=22033 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_22033 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14939

Test results coming soon (I hope)...

Details

- notification for comment with ID 2577368019 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2025-01-08T10:59:38Z

Test report by @boegelbot
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/6682cd2e9008b81280976c6f4ca2c1ba for a full test report.

boegel · 2025-01-08T11:57:27Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-01-08T12:00:18Z

@boegel: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=22033 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22033 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5518

Test results coming soon (I hope)...

Details

- notification for comment with ID 2577495485 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2025-01-08T12:05:47Z

Test report by @boegelbot
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/82e29c36605d697816b47242fe54ac85 for a full test report.

…g, to avoid tripping pattern matching that suggests to use SOURCE_TAR_GZ instead

boegel · 2025-01-09T07:50:09Z

Test report by @boegel
SUCCESS
Build succeeded for 5 out of 5 (5 easyconfigs in total)
node3103.skitty.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.9.18
See https://gist.github.com/boegel/9d37e364caf31eba26c9041039405efc for a full test report.

boegel · 2025-01-14T15:42:17Z

Going in, thanks @pavelToman!

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

Closed

2 tasks

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

13a9af4

boegel requested changes Jan 8, 2025

View reviewed changes

Comment thread easybuild/easyconfigs/l/LIQA/LIQA-1.3.4-foss-2023a.eb Outdated

Comment thread easybuild/easyconfigs/s/scNanoGPS/scNanoGPS-1.1-foss-2023a.eb Outdated

Comment thread easybuild/easyconfigs/s/scNanoGPS/scNanoGPS-1.1-foss-2023a.eb Outdated

boegel added 2 commits January 8, 2025 11:00

don't use %(namelower)s template in LIQA easyconfig, just use 'liqa'

29a6c95

include annovar as dependency for scNanoGPS

2eb6589

boegel requested changes Jan 8, 2025

View reviewed changes

Comment thread easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0-Perl-5.36.1.eb Outdated

boegel added 2 commits January 8, 2025 11:01

add download instructions to annovar easyconfig

8214b07

drop Perl versionsuffix for annovar with GCCcore/12.3.0

6bc401b

boegel changed the title ~~{bio}[GCCcore/12.3.0,foss/2023a] scNanoGPS v1.1, LIQA v1.3.4, lifelines v0.28.0, ... w/ Perl 5.36.1~~ {bio}[GCCcore/12.3.0,foss/2023a] scNanoGPS v1.1, LIQA v1.3.4, lifelines v0.28.0, annovar v20200607, tabix v0.2.6 Jan 8, 2025

boegel added this to the release after 4.9.4 milestone Jan 8, 2025

boegel requested changes Jan 8, 2025

View reviewed changes

Comment thread easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-12.3.0.eb Outdated

don't use single quotes in download_instructions in annovar easyconfi…

1f71625

…g, to avoid tripping pattern matching that suggests to use SOURCE_TAR_GZ instead

boegel force-pushed the 20241216125917_new_pr_scNanoGPS11 branch from 78111c1 to 1f71625 Compare January 9, 2025 07:34

boegel approved these changes Jan 9, 2025

View reviewed changes

boegel merged commit 66c025b into easybuilders:develop Jan 14, 2025

boegel modified the milestones: release after 4.9.4, 5.0.0 Mar 18, 2025

Conversation

pavelToman commented Dec 16, 2024 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

github-actions Bot commented Dec 16, 2024 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Updated software annovar-20200607-GCCcore-12.3.0.eb

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

Updated software tabix-0.2.6-GCCcore-12.3.0.eb

Uh oh!

pavelToman commented Dec 16, 2024

Uh oh!

pavelToman commented Dec 16, 2024

Uh oh!

pavelToman commented Dec 16, 2024

Uh oh!

pavelToman commented Dec 16, 2024

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

boegel commented Jan 8, 2025

Uh oh!

boegelbot commented Jan 8, 2025

Uh oh!

boegelbot commented Jan 8, 2025

Uh oh!

Uh oh!

boegel commented Jan 8, 2025

Uh oh!

boegelbot commented Jan 8, 2025

Uh oh!

boegelbot commented Jan 8, 2025

Uh oh!

boegel commented Jan 9, 2025

Uh oh!

boegel commented Jan 14, 2025

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

pavelToman commented Dec 16, 2024 •

edited

Loading

github-actions Bot commented Dec 16, 2024 •

edited

Loading

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

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

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