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{bio}[GCCcore/12.3.0] PennCNV v1.0.5#21827

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branfosj merged 4 commits intoeasybuilders:developfrom
verdurin:20241111151527_new_pr_PennCNV105
Jul 19, 2025
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{bio}[GCCcore/12.3.0] PennCNV v1.0.5#21827
branfosj merged 4 commits intoeasybuilders:developfrom
verdurin:20241111151527_new_pr_PennCNV105

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(created using eb --new-pr)

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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/e0b048bb05199272293360ece1ebe654 for a full test report.

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Updated software PennCNV-1.0.5-GCCcore-12.3.0.eb

Diff against PennCNV-1.0.5-GCCcore-8.3.0.eb

easybuild/easyconfigs/p/PennCNV/PennCNV-1.0.5-GCCcore-8.3.0.eb

diff --git a/easybuild/easyconfigs/p/PennCNV/PennCNV-1.0.5-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/PennCNV/PennCNV-1.0.5-GCCcore-12.3.0.eb
index f181ddc27e..d69ae01991 100644
--- a/easybuild/easyconfigs/p/PennCNV/PennCNV-1.0.5-GCCcore-8.3.0.eb
+++ b/easybuild/easyconfigs/p/PennCNV/PennCNV-1.0.5-GCCcore-12.3.0.eb
@@ -10,17 +10,17 @@ description = """A free software tool for Copy Number Variation (CNV) detection
  it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format,
  it can also handle other types of SNP arrays and oligonucleotide arrays."""
 
-toolchain = {'name': 'GCCcore', 'version': '8.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 source_urls = ['https://github.com/WGLab/PennCNV/archive/']
 sources = ['v%(version)s.tar.gz']
 checksums = ['5afd31c4cd92802a1fdfb6eb8c3c70ba82a0292d99a14755ce2ba0630f294d1f']
 
 builddependencies = [
-    ('binutils', '2.32'),
+    ('binutils', '2.40'),
 ]
 
-dependencies = [('Perl', '5.30.0')]
+dependencies = [('Perl', '5.36.1')]
 
 # Extension is compiled for the local Perl installation, and then used by 
 # supplied scripts 
@@ -38,6 +38,8 @@ sanity_check_paths = {
     'dirs': [],
 }
 
+sanity_check_commands = ["detect_cnv.pl  2>&1 | grep '^Usage:'"]
+
 modextrapaths = {'PATH': ''}
 
 moduleclass = 'bio'

branfosj
branfosj previously approved these changes Jul 19, 2025
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@boegelbot please test @ jsc-zen3

@github-actions github-actions Bot added new and removed update labels Jul 19, 2025
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Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 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/9066b65ff4a9556920dcf9246ded502c for a full test report.

Comment thread easybuild/easyconfigs/p/PennCNV/PennCNV-1.0.5-GCCcore-12.3.0.eb Outdated
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@boegelbot please test @ jsc-zen3

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@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=21827 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21827 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 7294

Test results coming soon (I hope)...

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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).

@branfosj branfosj added this to the release after 5.1.1 milestone Jul 19, 2025
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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 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/f2e2cc5cb972c0af0545a1426894b902 for a full test report.

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Going in, thanks @verdurin!

@branfosj branfosj merged commit a33c99c into easybuilders:develop Jul 19, 2025
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3 participants