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add patch to fix dependency check in OPERA-MS#22725

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boegel merged 1 commit intoeasybuilders:developfrom
stevenvdb:20250407151645_new_pr_OPERA-MS09020240703
May 24, 2025
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add patch to fix dependency check in OPERA-MS#22725
boegel merged 1 commit intoeasybuilders:developfrom
stevenvdb:20250407151645_new_pr_OPERA-MS09020240703

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@stevenvdb stevenvdb commented Apr 7, 2025 •
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  • The command OPERA-MS check_dependency is executed as a sanity check. It will however revert an earlier created symlink to the correct perl interpreter. A patch is added to make sure the existing correct symlink is not removed.
  • Some paths are hardcoded in scripts such as tools_opera_ms/MUMmer3.23/exact-tandems during compilation. This is why the build is now done in the installation directory (buildininstalldir = True)

(created using eb --new-pr)

@github-actions github-actions Bot added the change label Apr 7, 2025
@boegel boegel changed the title Fix dependency check in OPERA-MS add patch to fix dependency check in OPERA-MS May 24, 2025
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boegel approved these changes May 24, 2025
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lgtm

@boegel boegel added bug fix and removed change labels May 24, 2025
@boegel boegel added this to the next release (5.1.0) milestone May 24, 2025
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boegel commented May 24, 2025

@boegelbot please test @ jsc-zen3

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boegel commented May 24, 2025

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (1 easyconfigs in total)
node3502.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/1c5d7d5bb5bcd622cbf910c15ede59a2 for a full test report.

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boegelbot commented May 24, 2025

@boegel: 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=22725 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22725 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 6479

Test results coming soon (I hope)...

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boegelbot commented May 24, 2025

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/08fe129f3d2f3421d8bb9e8a43853797 for a full test report.

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boegel commented May 24, 2025

Going in, thanks @stevenvdb!

@boegel boegel merged commit 6555bb0 into easybuilders:develop May 24, 2025
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