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fix PyVCF easyconfig, only supports Python 2#11437

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verdurin merged 1 commit intoeasybuilders:developfrom
boegel:PyVCF_Py2
Oct 5, 2020
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fix PyVCF easyconfig, only supports Python 2#11437
verdurin merged 1 commit intoeasybuilders:developfrom
boegel:PyVCF_Py2

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@boegel boegel commented Oct 5, 2020

I noticed that the PyVCF scripts had a hardcoded /software/Python/2.7.16-GCCcore-8.3.0/bin/python, so I enabled the use of fix_python_shebang_for to fix the scripts.

That led to a failing sanity check, with "vcf_sample_filter.py --help" failing with:

File "/software/PyVCF/0.6.8-GCC-8.3.0/bin/vcf_sample_filter.py", line 37
    print "Samples:"
                   ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Samples:")?

This shows that PyVCF is really only compatible with Python 2 (makes sense, sort of, last release was in March 2016...)

@boegel boegel added the bug fix label Oct 5, 2020
@boegel boegel added this to the next release (4.3.1) milestone Oct 5, 2020
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boegel commented Oct 5, 2020

@boegelbot please test @ generoso

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boegelbot commented Oct 5, 2020

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

PR test command 'EB_PR=11437 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_11437 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 8014

Test results coming soon (I hope)...

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- notification for comment with ID 703717541 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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boegel commented Oct 5, 2020

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in this PR)
node3170.skitty.os - Linux centos linux 7.8.2003, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/40ea3eb923bee474b8922bd1ad5731bc for a full test report.

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boegelbot commented Oct 5, 2020

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (2 easyconfigs in this PR)
generoso-x-2 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/e169cf4bfb041de116761be7e95b0780 for a full test report.

@boegel boegel requested a review from verdurin October 5, 2020 16:19
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verdurin commented Oct 5, 2020

Test report by @verdurin
SUCCESS
Build succeeded for 12 out of 12 (2 easyconfigs in this PR)
nuc.lan - Linux Fedora 32, x86_64, Intel(R) Core(TM) i7-8650U CPU @ 1.90GHz, Python 3.8.5
See https://gist.github.com/3c98b8afb6b2ff313813f4db84bb2918 for a full test report.

verdurin
verdurin approved these changes Oct 5, 2020
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Looks fine.

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verdurin commented Oct 5, 2020

Going in, thanks @boegel!

@verdurin verdurin merged commit a65b8f0 into easybuilders:develop Oct 5, 2020
@boegel boegel deleted the PyVCF_Py2 branch October 5, 2020 19:06
@seb45tian seb45tian mentioned this pull request Nov 30, 2020
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