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downgrade SPAdes dependency to v3.13.1 for Unicycler 0.4.9 since v3.15.3 is too new#15840

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jfgrimm merged 2 commits intoeasybuilders:developfrom
ysagon:20220712174026_new_pr_SPAdes3130
Jul 15, 2022
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downgrade SPAdes dependency to v3.13.1 for Unicycler 0.4.9 since v3.15.3 is too new#15840
jfgrimm merged 2 commits intoeasybuilders:developfrom
ysagon:20220712174026_new_pr_SPAdes3130

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@ysagon ysagon commented Jul 12, 2022

(created using eb --new-pr)

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ysagon commented Jul 12, 2022 

Dependencies:
  Program         Version   Status  
  spades.py       3.15.3    too new 
  racon           1.4.21    good    
  makeblastdb     2.11.0+   good    
  tblastn         2.11.0+   good    
  bowtie2-build   2.4.4     good    
  bowtie2         2.4.4     good    
  samtools        1.13      good    
  java            11.0.2    good    
  pilon           1.23      good    
  bcftools                  not used

Error: Unicycler requires SPAdes v3.6.2 - v3.13.0

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jfgrimm commented Jul 13, 2022

Test report by @jfgrimm
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node006.pri.viking.alces.network - Linux CentOS Linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6138 CPU @ 2.00GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/9c4f8f887b549785e317b9289084ff7f for a full test report.

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jfgrimm commented Jul 13, 2022

@ysagon it would be good to add a test that catches issues like this. Could you update the PR to add something like this?

_test_cmd = 'unicycler -t %(parallel)s -1 short_reads_1.fastq.gz -2 short_reads_2.fastq.gz -o outdir'
postinstallcmds = [
    ' '.join([
        "cd %(builddir)s/%(name)s-%(version)s/sample_data &&",
        "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH",
        "PATH=%(installdir)s/bin:$PATH",
        _test_cmd,
    ]),
]

@jfgrimm jfgrimm added this to the 4.x milestone Jul 13, 2022
@jfgrimm jfgrimm added the change label Jul 13, 2022
@jfgrimm jfgrimm mentioned this pull request Jul 14, 2022
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jfgrimm commented Jul 15, 2022

@boegelbot please test @ generoso

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boegelbot commented Jul 15, 2022

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

PR test command 'EB_PR=15840 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_15840 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 8874

Test results coming soon (I hope)...

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- notification for comment with ID 1185591039 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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boegelbot commented Jul 15, 2022

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
cns1 - 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/7b2d3bbc4c1cd16fc2db69b6d728e89c for a full test report.

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jfgrimm commented Jul 15, 2022

@boegelbot please test @ jsc-zen2

@jfgrimm jfgrimm modified the milestones: 4.x, next release (4.6.1?) Jul 15, 2022
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jfgrimm approved these changes Jul 15, 2022
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LGTM

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boegelbot commented Jul 15, 2022

@jfgrimm: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=15840 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_15840 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 1388

Test results coming soon (I hope)...

Details

- notification for comment with ID 1185607307 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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boegelbot commented Jul 15, 2022

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (2 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/2d2bcc7ea82a46f3915c042ed090d34e for a full test report.

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jfgrimm commented Jul 15, 2022

Going in, thanks @ysagon!

@jfgrimm jfgrimm merged commit 7cbc585 into easybuilders:develop Jul 15, 2022
@boegel boegel removed the bug report label Aug 6, 2022
@boegel boegel changed the title downgrade SPAdes: Unicycler 0.4.9 isn't working with upper SPAdes version downgrade SPAdes dependency to v3.13.1 for Unicycler 0.4.9 since v3.15.3 is too new Aug 6, 2022
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