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{bio}[GCC/12.3.0] Cluster-Buster v20240927 #21847

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merged 1 commit into from
Nov 29, 2024
Merged

{bio}[GCC/12.3.0] Cluster-Buster v20240927 #21847

merged 1 commit into from
Nov 29, 2024

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PetrKralCZ
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@PetrKralCZ PetrKralCZ commented Nov 13, 2024 •
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(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#439

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Updated software Cluster-Buster-20240927-GCC-12.3.0.eb

Diff against Cluster-Buster-20200507-GCC-12.2.0.eb

easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20200507-GCC-12.2.0.eb

diff --git a/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20200507-GCC-12.2.0.eb b/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20240927-GCC-12.3.0.eb
index 0636ef933a..752cc55bb9 100644
--- a/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20200507-GCC-12.2.0.eb
+++ b/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20240927-GCC-12.3.0.eb
@@ -1,23 +1,18 @@
 easyblock = 'MakeCp'
 
 name = 'Cluster-Buster'
-version = '20200507'
+version = '20240927'
+local_commit = '06fee8b'
 
 homepage = 'https://github.com/weng-lab/cluster-buster'
 description = """Cluster-Buster is a program for finding interesting functional regions,
  such as transcriptional enhancers, in DNA sequences."""
 
-toolchain = {'name': 'GCC', 'version': '12.2.0'}
-
-sources = [{
-    'git_config': {
-        'url': 'https://github.com/weng-lab',
-        'repo_name': '%(namelower)s',
-        'commit': 'ac1d33cffff0c276216450ebced471595cf01488',
-    },
-    'filename': SOURCE_TAR_GZ,
-}]
-checksums = [None]
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/weng-lab/cluster-buster/archive/']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCELOWER_TAR_GZ}]
+checksums = ['a77583ae1f38cc08af551932e5f6b35185fde78db330270bb2eb32ecb4d926cc']
 
 files_to_copy = [(['cbust'], 'bin')]
Diff against Cluster-Buster-20160106-intel-2016a.eb

easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20160106-intel-2016a.eb

diff --git a/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20160106-intel-2016a.eb b/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20240927-GCC-12.3.0.eb
index 009a6c2057..752cc55bb9 100644
--- a/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20160106-intel-2016a.eb
+++ b/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20240927-GCC-12.3.0.eb
@@ -1,19 +1,18 @@
-easyblock = 'CmdCp'
+easyblock = 'MakeCp'
 
 name = 'Cluster-Buster'
-version = '20160106'
+version = '20240927'
+local_commit = '06fee8b'
 
-homepage = 'https://github.com/weng-lab/cluster-buster/'
-description = """Cluster-Buster: Finding dense clusters of motifs in DNA sequences"""
+homepage = 'https://github.com/weng-lab/cluster-buster'
+description = """Cluster-Buster is a program for finding interesting functional regions,
+ such as transcriptional enhancers, in DNA sequences."""
 
-source_urls = ['https://github.com/weng-lab/cluster-buster/archive/']
-sources = ['a343491.tar.gz']
-
-toolchain = {'name': 'intel', 'version': '2016a'}
-
-start_dir = 'cbust-src'
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
 
-cmds_map = [('.*', "$CXX $CXXFLAGS -DNDEBUG -o cbust *.cpp")]
+source_urls = ['https://github.com/weng-lab/cluster-buster/archive/']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCELOWER_TAR_GZ}]
+checksums = ['a77583ae1f38cc08af551932e5f6b35185fde78db330270bb2eb32ecb4d926cc']
 
 files_to_copy = [(['cbust'], 'bin')]
 
@@ -22,4 +21,6 @@ sanity_check_paths = {
     'dirs': [],
 }
 
+sanity_check_commands = ['cbust -h']
+
 moduleclass = 'bio'

@PetrKralCZ PetrKralCZ mentioned this pull request Nov 13, 2024
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@boegelbot please test @ generoso

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

PR test command 'EB_PR=21847 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21847 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 14702

Test results coming soon (I hope)...

- notification for comment with ID 2473495729 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).

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Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 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/146dc1566b6b62015411b3b5269e9269 for a full test report.

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@boegelbot please test @ jsc-zen3

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@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=21847 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21847 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 5264

Test results coming soon (I hope)...

- notification for comment with ID 2473510233 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).

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Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/bd9f7aeca4eb63428e7cd21718cd192e for a full test report.

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Test report by @verdurin
SUCCESS
Build succeeded for 1 out of 1 (1 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/7d3d4a8282af9cb262b73f36898bc3aa for a full test report.

verdurin
verdurin approved these changes Nov 29, 2024
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Looks fine.

@verdurin verdurin added this to the release after 4.9.4 milestone Nov 29, 2024
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Going in, thanks @PetrKralCZ!

@verdurin verdurin merged commit 03f426b into easybuilders:develop Nov 29, 2024
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Cluster-Buster
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