{bio}[GCCcore/12.3.0,foss/2023a] CheckM v1.0.18, DendroPy v4.5.2 w/ Python 2.7.18 by PetrKralCZ · Pull Request #22362 · easybuilders/easybuild-easyconfigs

PetrKralCZ · 2025-02-21T13:14:41Z

(created using eb --new-pr)
Needs:

{bio,lang}[GCC/12.3.0,GCCcore/12.3.0] Pysam v0.20.0, Cython v0.29.37 w/ Python 2.7.18 #22354
{lang,vis}[GCCcore/12.3.0,foss/2023a] matplotlib v2.2.5, Tkinter v2.7.18 w/ Python 2.7.18 #22355

…Py-4.5.2-GCCcore-12.3.0-Python-2.7.18.eb

github-actions · 2025-02-21T13:33:38Z

Updated software `CheckM-1.0.18-foss-2023a-Python-2.7.18.eb`

Diff against CheckM-1.2.2-foss-2022a.eb

easybuild/easyconfigs/c/CheckM/CheckM-1.2.2-foss-2022a.eb

diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.2.2-foss-2022a.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2023a-Python-2.7.18.eb
index a46bf26199..5103295826 100644
--- a/easybuild/easyconfigs/c/CheckM/CheckM-1.2.2-foss-2022a.eb
+++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2023a-Python-2.7.18.eb
@@ -1,40 +1,57 @@
 # Updated from previous config
 # Author: Pavel Grochal (INUITS)
-# Updated by: Filip Kružík (INUITS)
 # License: GPLv2
+# Update: Petr Král (INUITS)
 
 easyblock = 'PythonPackage'
 
 name = 'CheckM'
-version = '1.2.2'
+version = '1.0.18'
+versionsuffix = '-Python-%(pyver)s'
 
 homepage = 'https://github.com/Ecogenomics/CheckM'
-description = """CheckM provides a set of tools for assessing the quality of genomes recovered from isolates,
- single cells, or metagenomes."""
+description = """CheckM provides a set of tools for assessing the quality of
+genomes recovered from isolates, single cells, or metagenomes."""
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
-source_urls = ['https://github.com/Ecogenomics/CheckM/archive']
-sources = ['v%(version)s.tar.gz']
-checksums = ['a748b94e93f8d5fecfd0d5b3f17fcb119b25d4b45217e047b2fd742b21e74c0e']
+source_urls = [
+    'https://pypi.python.org/packages/source/c/checkm-genome',
+    'https://data.ace.uq.edu.au/public/CheckM_databases/',
+]
+sources = [
+    'checkm-genome-%(version)s.tar.gz',
+    {
+        'filename': 'checkm_data_2015_01_16.tar.gz',
+        'extract_cmd': "mkdir -p %(builddir)s/data && cd %(builddir)s/data && tar xfvz %s",
+    },
+]
+checksums = [
+    '0dcf31eab5e340a0fff37d7a5091d46d9269b0708db8f789adcd7cbd2a09a2b7',  # checkm-genome-1.0.18.tar.gz
+    '971ec469348bd6c3d9eb96142f567f12443310fa06c1892643940f35f86ac92c',  # checkm_data_2015_01_16.tar.gz
+]
 
-# Dependencies:
-# https://github.com/Ecogenomics/CheckM/blob/master/setup.py
 dependencies = [
-    ('Python', '3.10.4'),
+    ('Python', '2.7.18'),
     ('pplacer', '1.1.alpha19', '', SYSTEM),
     ('prodigal', '2.6.3'),
-    ('HMMER', '3.3.2'),
-    ('SciPy-bundle', '2022.05'),  # numpy
-    ('matplotlib', '3.5.2'),
-    ('Pysam', '0.19.1'),
-    ('DendroPy', '4.5.2'),
-    ('CheckM-Database', '2015_01_16', '', SYSTEM),
+    ('HMMER', '3.4'),
+    ('SciPy-bundle', '2024.06', versionsuffix),
+    ('matplotlib', '2.2.5', versionsuffix),
+    ('Pysam', '0.20.0', versionsuffix),
+    ('DendroPy', '4.5.2', versionsuffix),
 ]
 
 download_dep_fail = True
 use_pip = True
 
+# also install CheckM databases, see https://github.com/Ecogenomics/CheckM/wiki/Installation#how-to-install-checkm
+postinstallcmds = [
+    "cp -a %(builddir)s/data %(installdir)s",
+    "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH "
+    "%(installdir)s/bin/checkm data setRoot %(installdir)s/data",
+]
+
 sanity_check_paths = {
     'files': ['bin/checkm'],
     'dirs': ['lib/python%(pyshortver)s/site-packages'],

Diff against CheckM-1.1.3-foss-2021b.eb

easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021b.eb

diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021b.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2023a-Python-2.7.18.eb
index 9cf5f49131..5103295826 100644
--- a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021b.eb
+++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2023a-Python-2.7.18.eb
@@ -1,18 +1,19 @@
 # Updated from previous config
 # Author: Pavel Grochal (INUITS)
-# Updated by: Filip Kružík (INUITS)
 # License: GPLv2
+# Update: Petr Král (INUITS)
 
 easyblock = 'PythonPackage'
 
 name = 'CheckM'
-version = '1.1.3'
+version = '1.0.18'
+versionsuffix = '-Python-%(pyver)s'
 
 homepage = 'https://github.com/Ecogenomics/CheckM'
-description = """CheckM provides a set of tools for assessing the quality of genomes recovered from isolates,
- single cells, or metagenomes."""
+description = """CheckM provides a set of tools for assessing the quality of
+genomes recovered from isolates, single cells, or metagenomes."""
 
-toolchain = {'name': 'foss', 'version': '2021b'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 source_urls = [
     'https://pypi.python.org/packages/source/c/checkm-genome',
@@ -26,21 +27,19 @@ sources = [
     },
 ]
 checksums = [
-    '7fda369783d3b7d6a7324ee33cc93ac3560fba509bf2139e920fa661e2b45644',  # checkm-genome-1.1.3.tar.gz
+    '0dcf31eab5e340a0fff37d7a5091d46d9269b0708db8f789adcd7cbd2a09a2b7',  # checkm-genome-1.0.18.tar.gz
     '971ec469348bd6c3d9eb96142f567f12443310fa06c1892643940f35f86ac92c',  # checkm_data_2015_01_16.tar.gz
 ]
 
-# Dependencies:
-# https://github.com/Ecogenomics/CheckM/blob/master/setup.py
 dependencies = [
-    ('Python', '3.9.6'),
+    ('Python', '2.7.18'),
     ('pplacer', '1.1.alpha19', '', SYSTEM),
     ('prodigal', '2.6.3'),
-    ('HMMER', '3.3.2'),
-    ('SciPy-bundle', '2021.10'),  # numpy
-    ('matplotlib', '3.4.3'),
-    ('Pysam', '0.17.0'),
-    ('DendroPy', '4.5.2'),
+    ('HMMER', '3.4'),
+    ('SciPy-bundle', '2024.06', versionsuffix),
+    ('matplotlib', '2.2.5', versionsuffix),
+    ('Pysam', '0.20.0', versionsuffix),
+    ('DendroPy', '4.5.2', versionsuffix),
 ]
 
 download_dep_fail = True

Diff against CheckM-1.1.3-foss-2021a.eb

easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021a.eb

diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021a.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2023a-Python-2.7.18.eb
index 7fb4d44716..5103295826 100644
--- a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021a.eb
+++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2023a-Python-2.7.18.eb
@@ -1,17 +1,19 @@
 # Updated from previous config
 # Author: Pavel Grochal (INUITS)
 # License: GPLv2
+# Update: Petr Král (INUITS)
 
 easyblock = 'PythonPackage'
 
 name = 'CheckM'
-version = '1.1.3'
+version = '1.0.18'
+versionsuffix = '-Python-%(pyver)s'
 
 homepage = 'https://github.com/Ecogenomics/CheckM'
-description = """CheckM provides a set of tools for assessing the quality of genomes recovered from isolates,
- single cells, or metagenomes."""
+description = """CheckM provides a set of tools for assessing the quality of
+genomes recovered from isolates, single cells, or metagenomes."""
 
-toolchain = {'name': 'foss', 'version': '2021a'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 source_urls = [
     'https://pypi.python.org/packages/source/c/checkm-genome',
@@ -25,21 +27,19 @@ sources = [
     },
 ]
 checksums = [
-    '7fda369783d3b7d6a7324ee33cc93ac3560fba509bf2139e920fa661e2b45644',  # checkm-genome-1.1.3.tar.gz
+    '0dcf31eab5e340a0fff37d7a5091d46d9269b0708db8f789adcd7cbd2a09a2b7',  # checkm-genome-1.0.18.tar.gz
     '971ec469348bd6c3d9eb96142f567f12443310fa06c1892643940f35f86ac92c',  # checkm_data_2015_01_16.tar.gz
 ]
 
-# Dependencies:
-# https://github.com/Ecogenomics/CheckM/blob/master/setup.py
 dependencies = [
-    ('Python', '3.9.5'),
+    ('Python', '2.7.18'),
     ('pplacer', '1.1.alpha19', '', SYSTEM),
     ('prodigal', '2.6.3'),
-    ('HMMER', '3.3.2'),
-    ('SciPy-bundle', '2021.05'),  # numpy
-    ('matplotlib', '3.4.2'),
-    ('Pysam', '0.16.0.1'),
-    ('DendroPy', '4.5.2'),
+    ('HMMER', '3.4'),
+    ('SciPy-bundle', '2024.06', versionsuffix),
+    ('matplotlib', '2.2.5', versionsuffix),
+    ('Pysam', '0.20.0', versionsuffix),
+    ('DendroPy', '4.5.2', versionsuffix),
 ]
 
 download_dep_fail = True

Updated software `DendroPy-4.5.2-GCCcore-12.3.0-Python-2.7.18.eb`

Diff against DendroPy-4.6.1-GCCcore-12.3.0.eb

easybuild/easyconfigs/d/DendroPy/DendroPy-4.6.1-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.6.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-12.3.0-Python-2.7.18.eb
index 1241b1fec4..6a9e4bd704 100644
--- a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.6.1-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-12.3.0-Python-2.7.18.eb
@@ -7,10 +7,12 @@
 # $Id$
 #
 ##
+# Update: Petr Král (INUITS)
 easyblock = 'PythonPackage'
 
 name = 'DendroPy'
-version = '4.6.1'
+version = '4.5.2'
+versionsuffix = '-Python-%(pyver)s'
 
 homepage = 'https://dendropy.org/'
 description = """A Python library for phylogenetics and phylogenetic computing: 
@@ -20,11 +22,11 @@ reading, writing, simulation, processing and manipulation of phylogenetic trees
 toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 sources = [SOURCE_TAR_GZ]
-checksums = ['26fcbe1cb5831301e8f1f2e15a0563620f0b8e29e6d409dd6a2a7c957dd64c16']
+checksums = ['3e5d2522170058ebc8d1ee63a7f2d25b915e34957dc02693ebfdc15f347a0101']
 
 builddependencies = [('binutils', '2.40')]
 
-dependencies = [('Python', '3.11.3')]
+dependencies = [('Python', '2.7.18')]
 
 download_dep_fail = True
 use_pip = True

Diff against DendroPy-4.5.2-GCCcore-12.2.0.eb

easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-12.3.0-Python-2.7.18.eb
index ea5696314d..6a9e4bd704 100644
--- a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-12.3.0-Python-2.7.18.eb
@@ -7,24 +7,26 @@
 # $Id$
 #
 ##
+# Update: Petr Král (INUITS)
 easyblock = 'PythonPackage'
 
 name = 'DendroPy'
 version = '4.5.2'
+versionsuffix = '-Python-%(pyver)s'
 
 homepage = 'https://dendropy.org/'
 description = """A Python library for phylogenetics and phylogenetic computing: 
 reading, writing, simulation, processing and manipulation of phylogenetic trees 
 (phylogenies) and characters."""
 
-toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 sources = [SOURCE_TAR_GZ]
 checksums = ['3e5d2522170058ebc8d1ee63a7f2d25b915e34957dc02693ebfdc15f347a0101']
 
-builddependencies = [('binutils', '2.39')]
+builddependencies = [('binutils', '2.40')]
 
-dependencies = [('Python', '3.10.8')]
+dependencies = [('Python', '2.7.18')]
 
 download_dep_fail = True
 use_pip = True

Diff against DendroPy-4.5.2-GCCcore-11.3.0.eb

easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-12.3.0-Python-2.7.18.eb
index 1ffdbf30d5..6a9e4bd704 100644
--- a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-12.3.0-Python-2.7.18.eb
@@ -7,24 +7,26 @@
 # $Id$
 #
 ##
+# Update: Petr Král (INUITS)
 easyblock = 'PythonPackage'
 
 name = 'DendroPy'
 version = '4.5.2'
+versionsuffix = '-Python-%(pyver)s'
 
 homepage = 'https://dendropy.org/'
 description = """A Python library for phylogenetics and phylogenetic computing: 
 reading, writing, simulation, processing and manipulation of phylogenetic trees 
 (phylogenies) and characters."""
 
-toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 sources = [SOURCE_TAR_GZ]
 checksums = ['3e5d2522170058ebc8d1ee63a7f2d25b915e34957dc02693ebfdc15f347a0101']
 
-builddependencies = [('binutils', '2.38')]
+builddependencies = [('binutils', '2.40')]
 
-dependencies = [('Python', '3.10.4')]
+dependencies = [('Python', '2.7.18')]
 
 download_dep_fail = True
 use_pip = True

…1018

PetrKralCZ · 2025-02-25T08:14:03Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-02-25T08:20:09Z

@PetrKralCZ: 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=22362 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22362 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5774

Test results coming soon (I hope)...

Details

- notification for comment with ID 2681059358 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 · 2025-02-25T08:26:35Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 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/badfb42fd5bd8f5f4c55a85ec8bb4ced for a full test report.

verdurin · 2025-02-26T09:41:58Z

Test report by @verdurin
SUCCESS
Build succeeded for 4 out of 4 (2 easyconfigs in total)
easybuild-el8.cloud.in.bmrc.ox.ac.uk - Linux Rocky Linux 8.10, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/verdurin/d9bf65f59f085232a52cb38079191753 for a full test report.

verdurin

Looks fine.

verdurin · 2025-02-26T09:44:36Z

@PetrKralCZ normally I would mention the removal of previous attributions, but given it's one of your colleagues, I guess that's your business...

PetrKralCZ · 2025-02-26T09:58:44Z

@PetrKralCZ normally I would mention the removal of previous attributions, but given it's one of your colleagues, I guess that's your business...

I used CheckM-1.0.18-foss-2020b-Python-2.7.18.eb as the base for CheckM-1.0.18-foss-2023a-Python-2.7.18.eb since both use the same version of CheckM with the same version of Python. I didn't remove any attribution. Only if you compared it to CheckM-1.2.2-foss-2022a.eb or something, that would make it look like I did.

boegel · 2025-03-02T14:27:03Z

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node3614.doduo.os - Linux RHEL 9.4, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.9.18
See https://gist.github.com/boegel/df810e909bea7718e7a76b0060278832 for a full test report.

branfosj · 2025-03-03T12:14:41Z

Test report by @branfosj
SUCCESS
Build succeeded for 4 out of 4 (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/776286da633f362cc7ae449ba4bce39d for a full test report.

branfosj · 2025-03-03T12:49:58Z

Going in, thanks @PetrKralCZ!

adding easyconfigs: CheckM-1.0.18-foss-2023a-Python-2.7.18.eb, Dendro…

36b947a

…Py-4.5.2-GCCcore-12.3.0-Python-2.7.18.eb

PetrKralCZ added the update label Feb 21, 2025

PetrKralCZ mentioned this pull request Feb 21, 2025

MetaWRAP vscentrum/vsc-software-stack#494

Closed

Merge branch 'easybuilders:develop' into 20250221141437_new_pr_CheckM…

16912c6

…1018

verdurin approved these changes Feb 26, 2025

View reviewed changes

PetrKralCZ mentioned this pull request Mar 3, 2025

{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

Merged

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

branfosj merged commit 4625d0d 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}[GCCcore/12.3.0,foss/2023a] CheckM v1.0.18, DendroPy v4.5.2 w/ Python 2.7.18#22362

{bio}[GCCcore/12.3.0,foss/2023a] CheckM v1.0.18, DendroPy v4.5.2 w/ Python 2.7.18#22362
branfosj merged 2 commits intoeasybuilders:developfrom
PetrKralCZ:20250221141437_new_pr_CheckM1018

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Updated software CheckM-1.0.18-foss-2023a-Python-2.7.18.eb

Updated software DendroPy-4.5.2-GCCcore-12.3.0-Python-2.7.18.eb

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PetrKralCZ commented Feb 21, 2025 •

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Updated software `CheckM-1.0.18-foss-2023a-Python-2.7.18.eb`

Updated software `DendroPy-4.5.2-GCCcore-12.3.0-Python-2.7.18.eb`