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{bio}[GCC/10.3.0] CAT-BAT v5.2.3 w/ Python 3.9.5#16577

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boegel merged 3 commits intoeasybuilders:developfrom
sib-swiss:20221108120216_new_pr_CAT-BAT523
Nov 9, 2022
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{bio}[GCC/10.3.0] CAT-BAT v5.2.3 w/ Python 3.9.5#16577
boegel merged 3 commits intoeasybuilders:developfrom
sib-swiss:20221108120216_new_pr_CAT-BAT523

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@SIB-software
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(created using eb --new-pr)

@smoretti smoretti added new BioHack2022 Related to EU BioHackathon 2022 labels Nov 8, 2022
@boegel boegel added this to the 4.x milestone Nov 8, 2022
sources = ['v%(version)s.tar.gz']
checksums = ['19a8eb28c0ebd3fc5a04b006d305a916dd1af00a32b70d2f30df35f32ca2929b']

builddependencies = [('binutils', '2.36.1')]
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binutils is not required when using GCC as toolchain (only required when using GCCcore toolchain)

postinstallcmds = ["cd %(installdir)s/ && ln -s CAT_pack bin && "
"chmod a+rx %(installdir)s/CAT_pack/*.py && "
"sed -i 's@/usr/bin/env/ python3@/usr/bin/env python3@' "
"%(installdir)s/CAT_pack/check.py"]
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Please use separate commands (easier to tell which command failed if one of them fails):

postinstallcmds = [
    "cd %(installdir)s/ && ln -s CAT_pack bin",
    "chmod a+rx %(installdir)s/CAT_pack/*.py",
    "sed -i 's@/usr/bin/env/ python3@/usr/bin/env python3@' %(installdir)s/CAT_pack/check.py",
]

BTW, that last sed commands doesn't actually change anything?

}

modextrapaths = {
'PATH': '',
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if CAT is in the CAT_pack subdir, this seems wrong?

postinstallcmds = [
"cd %(installdir)s/ && ln -s CAT_pack bin",
"chmod a+rx %(installdir)s/CAT_pack/*.py",
"sed -i 's@/usr/bin/env/ python3@/usr/bin/env python3@' %(installdir)s/CAT_pack/check.py",
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@smoretti Let's add a comment on top here to clarify what this does, because it's too easy to overlook:

Suggested change
"sed -i 's@/usr/bin/env/ python3@/usr/bin/env python3@' %(installdir)s/CAT_pack/check.py",
# fix shebang in check.py script ('/env/' should be '/env')
"sed -i 's@/usr/bin/env/ python3@/usr/bin/env python3@' %(installdir)s/CAT_pack/check.py",

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I forgot it

@boegel
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boegel commented Nov 9, 2022

@boegelbot please test @ generoso

]

sanity_check_paths = {
'files': ['CAT_pack/CAT', 'README.md'],
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Maybe also check for bin/CAT here, to verify the symlink that we put in place (it also helps point out why modextrapaths is not needed to make the sanity check command work)

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

PR test command 'EB_PR=16577 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_16577 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 9462

Test results coming soon (I hope)...

Details

- notification for comment with ID 1308327020 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)
cns2 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/0a42d4aeeb74cc82d484a301cd6164f4 for a full test report.

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boegel commented Nov 9, 2022

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (1 easyconfigs in total)
node3135.skitty.os - Linux RHEL 8.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/d24cb9f93970d83247832c969bce9cd5 for a full test report.

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boegel commented Nov 9, 2022

Going in, thanks @SIB-software!

@boegel boegel merged commit 027b4a7 into easybuilders:develop Nov 9, 2022
@smoretti smoretti deleted the 20221108120216_new_pr_CAT-BAT523 branch November 9, 2022 14:15
@boegel boegel modified the milestones: 4.x, next release (4.6.3?) Nov 9, 2022
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4 participants