{bio}[foss/2023a] Verkko v2.2.1, GraphAligner v1.0.20, Winnowmap v2.03, ... by pavelToman · Pull Request #22246 · easybuilders/easybuild-easyconfigs

pavelToman · 2025-01-31T13:27:24Z

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#495

…oss-2023a.eb, Winnowmap-2.03-GCCcore-12.3.0.eb, MashMap-3.1.3-GCC-12.3.0.eb and patches: GraphAligner-1.0.20_fix-makefile.patch

github-actions · 2025-01-31T13:27:51Z

Updated software `Winnowmap-2.03-GCCcore-12.3.0.eb`

Diff against Winnowmap-1.0-GCC-8.3.0.eb

easybuild/easyconfigs/w/Winnowmap/Winnowmap-1.0-GCC-8.3.0.eb

diff --git a/easybuild/easyconfigs/w/Winnowmap/Winnowmap-1.0-GCC-8.3.0.eb b/easybuild/easyconfigs/w/Winnowmap/Winnowmap-2.03-GCCcore-12.3.0.eb
index 10d33e589e..7f487379a7 100644
--- a/easybuild/easyconfigs/w/Winnowmap/Winnowmap-1.0-GCC-8.3.0.eb
+++ b/easybuild/easyconfigs/w/Winnowmap/Winnowmap-2.03-GCCcore-12.3.0.eb
@@ -1,22 +1,28 @@
 easyblock = 'MakeCp'
 
 name = 'Winnowmap'
-version = '1.0'
+version = '2.03'
 
 homepage = 'https://github.com/marbl/Winnowmap'
 description = """Winnowmap is a long-read mapping algorithm, and a result of our exploration
  into superior minimizer sampling techniques."""
 
-toolchain = {'name': 'GCC', 'version': '8.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 source_urls = ['https://github.com/marbl/Winnowmap/archive/']
 sources = ['v%(version)s.tar.gz']
-checksums = ['a1ce84052fe61af1376b199daff7bd5b1ddeff7d1bab3d61e88f184140117d14']
+checksums = ['f6375960ee2184b68c0f56d3ca95e12ec3218f9e44aeecbdb14f85f581112c83']
 
-files_to_copy = [(['computeHighFreqKmers', 'winnowmap'], 'bin')]
+builddependencies = [('binutils', '2.40')]
+dependencies = [('jemalloc', '5.3.0')]
+
+# fix - not use sysctl.h - not works on RHEL9 systems
+prebuildopts = "sed -i '36,39d' ext/meryl/src/utility/src/utility/system.C && "
+
+files_to_copy = ['bin', 'lib']
 
 sanity_check_paths = {
-    'files': ['bin/computeHighFreqKmers', 'bin/winnowmap'],
+    'files': ['bin/meryl', 'bin/winnowmap'],
     'dirs': [],
 }

pavelToman · 2025-01-31T13:29:26Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-01-31T13:30:08Z

@pavelToman: 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=22246 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22246 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5649

Test results coming soon (I hope)...

Details

- notification for comment with ID 2627344656 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 · 2025-01-31T13:33:44Z

Test report by @boegelbot
FAILED
Build succeeded for 2 out of 4 (4 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/c3f13afb44669121e1b1c825121ef50a for a full test report.

pavelToman · 2025-01-31T13:37:31Z

Test report by @pavelToman
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
node4006.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/5b40f19fb25ad85040bbbaa6cf66299c for a full test report.

pavelToman · 2025-02-03T10:27:36Z

Test report by @boegelbot FAILED Build succeeded for 2 out of 4 (4 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/c3f13afb44669121e1b1c825121ef50a for a full test report.

Problem with sysctl.h on RHEL9 systems - need to fix winnowmap easyconfig to not use it.
Prblem is there: https://github.com/marbl/Winnowmap/blob/26a9ad144cb35a55bf888ad26ddf5a19311b04ac/ext/meryl/src/utility/src/utility/system.C#L37

pavelToman · 2025-02-03T10:30:32Z

@boegelbot please test @ jsc-zen3

pavelToman · 2025-02-03T10:35:17Z

Test report by @pavelToman
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
node3121.skitty.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.9.18
See https://gist.github.com/pavelToman/9867536f2a6917fc3b0209de20d04220 for a full test report.

pavelToman · 2025-02-03T10:38:51Z

Test report by @pavelToman
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
node4016.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/1880811a3590548596b13a59cbc5d6ca for a full test report.

boegelbot · 2025-02-03T10:40:09Z

@pavelToman: 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=22246 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22246 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5657

Test results coming soon (I hope)...

Details

- notification for comment with ID 2630550196 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).

pavelToman · 2025-02-03T10:42:49Z

Test report by @pavelToman
SUCCESS
Build succeeded for 4 out of 4 (4 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/0e32e643e3ae65abb16d07e15becf65b for a full test report.

boegelbot · 2025-02-03T10:45:33Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (4 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/ff3525f5a8fc62c89b1286470ab3481e for a full test report.

boegel · 2025-02-18T12:09:35Z

Test report by @boegel
SUCCESS
Build succeeded for 6 out of 6 (4 easyconfigs in total)
node3100.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/137fda0eeee34f92fd87f5c00b329c47 for a full test report.

boegel

lgtm

boegel · 2025-02-18T12:17:24Z

Going in, thanks @pavelToman!

adding easyconfigs: Verkko-2.2.1-foss-2023a.eb, GraphAligner-1.0.20-f…

8108e12

…oss-2023a.eb, Winnowmap-2.03-GCCcore-12.3.0.eb, MashMap-3.1.3-GCC-12.3.0.eb and patches: GraphAligner-1.0.20_fix-makefile.patch

pavelToman added new update labels Jan 31, 2025

pavelToman mentioned this pull request Jan 31, 2025

Verkko vscentrum/vsc-software-stack#495

Closed

pavelToman removed the update label Jan 31, 2025

fix sysctl.h + BWA version

d2f5b59

github-actions Bot added the update label Feb 3, 2025

pavelToman added 2 commits February 3, 2025 12:10

add patch description

e3b0979

fix GraphAlinger patch checksum

6695945

boegel approved these changes Feb 18, 2025

View reviewed changes

boegel added this to the release after 4.9.4 milestone Feb 18, 2025

boegel merged commit cfe2f8d into easybuilders:develop Feb 18, 2025

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

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Updated software Winnowmap-2.03-GCCcore-12.3.0.eb

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Updated software `Winnowmap-2.03-GCCcore-12.3.0.eb`

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