{bio}[GCC/12.3.0,GCCcore/12.3.0,foss/2023a] CONCOCT v1.1.0, MEGAHIT v1.2.9, BEDTools v2.31.0 w/ Python 2.7.18 by PetrKralCZ · Pull Request #22431 · easybuilders/easybuild-easyconfigs

PetrKralCZ · 2025-03-03T10:20:49Z

Needs:

…T-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb, BEDTools-2.31.0-GCC-12.3.0-Python-2.7.18.eb

github-actions · 2025-03-03T10:21:27Z

Updated software `CONCOCT-1.1.0-foss-2023a-Python-2.7.18.eb`

Diff against CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb

easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb

diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2023a-Python-2.7.18.eb
index e8a5cb71f3..e8b6076f54 100644
--- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb
+++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2023a-Python-2.7.18.eb
@@ -1,4 +1,4 @@
-easyblock = 'PythonPackage'
+easyblock = 'PythonBundle'
 
 name = 'CONCOCT'
 version = '1.1.0'
@@ -10,30 +10,36 @@ 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': '2020b'}
-
-source_urls = ['https://github.com/BinPro/CONCOCT/archive/']
-sources = ['%(version)s.tar.gz']
-checksums = ['00aecacb4b720ac123a63e65072c61e0b5a8690d844c869aaee4dbf287c82888']
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 dependencies = [
     ('Python', '2.7.18'),
-    ('BEDTools', '2.30.0'),
+    ('BEDTools', '2.31.0'),
     ('Biopython', '1.76', versionsuffix),
-    ('Bowtie2', '2.4.2'),
+    ('Bowtie2', '2.5.4', versionsuffix),
     ('CheckM', '1.0.18', versionsuffix),
-    ('GSL', '2.6'),
+    ('GSL', '2.7'),
     ('MEGAHIT', '1.2.9', versionsuffix),
-    ('parallel', '20210322'),
-    ('picard', '2.25.0', '-Java-11', SYSTEM),
-    ('Pysam', '0.16.0.1', versionsuffix),
-    ('SAMtools', '1.11'),
+    ('parallel', '20230722'),
+    ('picard', '2.25.1', '-Java-11', SYSTEM),
+    ('Pysam', '0.20.0', versionsuffix),
+    ('SAMtools', '1.18'),
     ('scikit-learn', '0.20.4', versionsuffix),
 ]
 
-download_dep_fail = True
-
 use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('nose', '1.3.7', {
+        'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'],
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/BinPro/CONCOCT/archive/'],
+        'sources': ['%(version)s.tar.gz'],
+        'checksums': ['00aecacb4b720ac123a63e65072c61e0b5a8690d844c869aaee4dbf287c82888'],
+    }),
+]
 
 sanity_check_paths = {
     'files': ['bin/concoct'],
@@ -42,6 +48,4 @@ sanity_check_paths = {
 
 sanity_check_commands = ["concoct --help"]
 
-sanity_pip_check = True
-
 moduleclass = 'bio'

Diff against CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb

easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb

diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2023a-Python-2.7.18.eb
index f1334d88a2..e8b6076f54 100644
--- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb
+++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2023a-Python-2.7.18.eb
@@ -1,47 +1,51 @@
-# Updated from previous config
-# Author: Pavel Grochal (INUITS)
-# License: GPLv2
-
-easyblock = 'PythonPackage'
+easyblock = 'PythonBundle'
 
 name = 'CONCOCT'
 version = '1.1.0'
 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': '2019a'}
+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."""
 
-source_urls = ['https://github.com/BinPro/CONCOCT/archive/']
-sources = ['%(version)s.tar.gz']
-checksums = ['00aecacb4b720ac123a63e65072c61e0b5a8690d844c869aaee4dbf287c82888']
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 dependencies = [
-    ('Python', '2.7.15'),
-    ('GSL', '2.5'),
-    # gslcblas
-    ('Biopython', '1.73'),
-    ('scikit-learn', '0.20.3'),
-    ('MEGAHIT', '1.2.8'),
-    ('BEDTools', '2.28.0'),
-    ('picard', '2.21.1', '-Java-11', True),
-    ('SAMtools', '1.9'),
-    ('Bowtie2', '2.3.5.1'),
-    ('parallel', '20190622'),
-    ('Pysam', '0.15.2'),
+    ('Python', '2.7.18'),
+    ('BEDTools', '2.31.0'),
+    ('Biopython', '1.76', versionsuffix),
+    ('Bowtie2', '2.5.4', versionsuffix),
     ('CheckM', '1.0.18', versionsuffix),
+    ('GSL', '2.7'),
+    ('MEGAHIT', '1.2.9', versionsuffix),
+    ('parallel', '20230722'),
+    ('picard', '2.25.1', '-Java-11', SYSTEM),
+    ('Pysam', '0.20.0', versionsuffix),
+    ('SAMtools', '1.18'),
+    ('scikit-learn', '0.20.4', versionsuffix),
 ]
 
-download_dep_fail = True
-
 use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('nose', '1.3.7', {
+        'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'],
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/BinPro/CONCOCT/archive/'],
+        'sources': ['%(version)s.tar.gz'],
+        'checksums': ['00aecacb4b720ac123a63e65072c61e0b5a8690d844c869aaee4dbf287c82888'],
+    }),
+]
 
 sanity_check_paths = {
     'files': ['bin/concoct'],
     'dirs': ['lib/python%(pyshortver)s/site-packages'],
 }
 
+sanity_check_commands = ["concoct --help"]
+
 moduleclass = 'bio'

Diff against CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb

easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb

diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2023a-Python-2.7.18.eb
index 30bfadb038..e8b6076f54 100644
--- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb
+++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2023a-Python-2.7.18.eb
@@ -1,43 +1,51 @@
-easyblock = 'PythonPackage'
+easyblock = 'PythonBundle'
 
 name = 'CONCOCT'
-version = '1.0.0'
+version = '1.1.0'
 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."""
+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'}
-
-source_urls = ['https://github.com/BinPro/CONCOCT/archive']
-sources = ['%(version)s.tar.gz']
-checksums = ['4428a1d7bce5c7546106bea0a0ff6c2168e3680f6422adce5ef523bce46dc180']
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 dependencies = [
-    ('Python', '3.6.3'),
-    ('GSL', '2.4'),
-    ('Biopython', '1.70', 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),
+    ('Python', '2.7.18'),
+    ('BEDTools', '2.31.0'),
+    ('Biopython', '1.76', versionsuffix),
+    ('Bowtie2', '2.5.4', versionsuffix),
+    ('CheckM', '1.0.18', versionsuffix),
+    ('GSL', '2.7'),
+    ('MEGAHIT', '1.2.9', versionsuffix),
+    ('parallel', '20230722'),
+    ('picard', '2.25.1', '-Java-11', SYSTEM),
+    ('Pysam', '0.20.0', versionsuffix),
+    ('SAMtools', '1.18'),
+    ('scikit-learn', '0.20.4', versionsuffix),
 ]
 
 use_pip = True
-download_dep_fail = True
-
-options = {'modulename': 'concoct'}
+sanity_pip_check = True
+
+exts_list = [
+    ('nose', '1.3.7', {
+        'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'],
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/BinPro/CONCOCT/archive/'],
+        'sources': ['%(version)s.tar.gz'],
+        'checksums': ['00aecacb4b720ac123a63e65072c61e0b5a8690d844c869aaee4dbf287c82888'],
+    }),
+]
 
 sanity_check_paths = {
-    'files': ['bin/concoct', 'bin/concoct_refine'],
-    'dirs': ['lib/python%(pyshortver)s/site-packages/concoct'],
+    'files': ['bin/concoct'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
 }
 
+sanity_check_commands = ["concoct --help"]
+
 moduleclass = 'bio'

Updated software `MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb`

Diff against MEGAHIT-1.2.9-GCCcore-12.2.0.eb

easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb
index 476de3749c..85769e3a07 100644
--- a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb
@@ -2,25 +2,26 @@ easyblock = 'CMakeMake'
 
 name = 'MEGAHIT'
 version = '1.2.9'
+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': 'GCCcore', 'version': '12.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 source_urls = ['https://github.com/voutcn/%(namelower)s/archive/']
 sources = ['v%(version)s.tar.gz']
 checksums = ['09026eb07cc4e2d24f58b0a13f7a826ae8bb73da735a47cb1cbe6e4693118852']
 
 builddependencies = [
-    ('binutils', '2.39'),
-    ('CMake', '3.24.3'),
-    ('zlib', '1.2.12'),
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+    ('zlib', '1.2.13'),
 ]
 
 dependencies = [
-    ('Python', '3.10.8'),
+    ('Python', '2.7.18'),
     ('bzip2', '1.0.8'),
     ('gzip', '1.12'),
 ]

Diff against MEGAHIT-1.2.9-GCCcore-12.3.0.eb

easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb
index 85eb10386d..85769e3a07 100644
--- a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb
@@ -2,6 +2,7 @@ easyblock = 'CMakeMake'
 
 name = 'MEGAHIT'
 version = '1.2.9'
+versionsuffix = '-Python-%(pyver)s'
 
 homepage = 'https://github.com/voutcn/megahit'
 description = """An ultra-fast single-node solution for large and complex
@@ -18,13 +19,13 @@ builddependencies = [
     ('CMake', '3.26.3'),
     ('zlib', '1.2.13'),
 ]
+
 dependencies = [
-    ('Python', '3.11.3'),
+    ('Python', '2.7.18'),
     ('bzip2', '1.0.8'),
     ('gzip', '1.12'),
 ]
 
-
 sanity_check_paths = {
     'files': [
         'bin/%(namelower)s',

Diff against MEGAHIT-1.2.9-GCCcore-11.3.0.eb

easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb
index 23927deb7b..85769e3a07 100644
--- a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb
@@ -2,25 +2,26 @@ easyblock = 'CMakeMake'
 
 name = 'MEGAHIT'
 version = '1.2.9'
+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': 'GCCcore', 'version': '11.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 source_urls = ['https://github.com/voutcn/%(namelower)s/archive/']
 sources = ['v%(version)s.tar.gz']
 checksums = ['09026eb07cc4e2d24f58b0a13f7a826ae8bb73da735a47cb1cbe6e4693118852']
 
 builddependencies = [
-    ('binutils', '2.38'),
-    ('CMake', '3.24.3'),
-    ('zlib', '1.2.12'),
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+    ('zlib', '1.2.13'),
 ]
 
 dependencies = [
-    ('Python', '3.10.4'),
+    ('Python', '2.7.18'),
     ('bzip2', '1.0.8'),
     ('gzip', '1.12'),
 ]

delete empty line

easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.0-GCC-12.3.0-Python-2.7.18.eb

branfosj · 2025-03-03T16:34:48Z

Test report by @branfosj
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
bear-pg0105u03a - Linux RHEL 8.10, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/branfosj/ae40d2966472cba63780ea9406430c6d for a full test report.

branfosj · 2025-03-03T17:02:43Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-03-03T17:10:09Z

@branfosj: 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=22431 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22431 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5838

Test results coming soon (I hope)...

Details

- notification for comment with ID 2695025977 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 · 2025-03-03T17:13:39Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
jsczen3c2.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/4ed68e94a63a8fca895953f9d2dcbbd2 for a full test report.

branfosj · 2025-03-03T17:15:14Z

Going in, thanks @PetrKralCZ!

adding easyconfigs: CONCOCT-1.1.0-foss-2023a-Python-2.7.18.eb, MEGAHI…

9697559

…T-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb, BEDTools-2.31.0-GCC-12.3.0-Python-2.7.18.eb

PetrKralCZ mentioned this pull request Mar 3, 2025

MetaWRAP vscentrum/vsc-software-stack#494

Closed

github-actions bot added the update label Mar 3, 2025

PetrKralCZ mentioned this pull request Mar 3, 2025

{bio}[foss/2023a] metaWRAP v1.4-20230728 w/ Python 2.7.18 #22432

Merged

PetrKralCZ added 2 commits March 3, 2025 11:30

add sanity check commands

54d709d

Update MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb

5f098ef

delete empty line

PetrKralCZ marked this pull request as ready for review March 3, 2025 11:32

branfosj requested changes Mar 3, 2025

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easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.0-GCC-12.3.0-Python-2.7.18.eb Outdated Show resolved Hide resolved

remove unnecessary dependency

42122db

branfosj approved these changes Mar 3, 2025

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branfosj added this to the release after 4.9.4 milestone Mar 3, 2025

branfosj merged commit 5054c2e into easybuilders:develop Mar 3, 2025
10 checks passed

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

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{bio}[GCC/12.3.0,GCCcore/12.3.0,foss/2023a] CONCOCT v1.1.0, MEGAHIT v1.2.9, BEDTools v2.31.0 w/ Python 2.7.18#22431

{bio}[GCC/12.3.0,GCCcore/12.3.0,foss/2023a] CONCOCT v1.1.0, MEGAHIT v1.2.9, BEDTools v2.31.0 w/ Python 2.7.18#22431
branfosj merged 4 commits intoeasybuilders:developfrom
PetrKralCZ:20250303110453_new_pr_CONCOCT110

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Updated software CONCOCT-1.1.0-foss-2023a-Python-2.7.18.eb

Updated software MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb

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Updated software `CONCOCT-1.1.0-foss-2023a-Python-2.7.18.eb`

Updated software `MEGAHIT-1.2.9-GCCcore-12.3.0-Python-2.7.18.eb`