{bio}[GCC/11.3.0,foss/2022a] alleleCount v4.2.1, ASCAT v3.1.2, alleleIntegrator v0.8.8 by ItIsI-Orient · Pull Request #17923 · easybuilders/easybuild-easyconfigs

ItIsI-Orient · 2023-05-18T18:58:38Z

(created using eb --new-pr)

…-2022a-R-4.2.1.eb, alleleIntegrator-0.8.8-foss-2022a-R-4.2.1.eb

ItIsI-Orient · 2023-05-18T19:53:33Z

@boegelbot please test @ generoso

boegelbot · 2023-05-18T19:55:13Z

@ItIsI-Orient: Request for testing this PR well received on login1

PR test command 'EB_PR=17923 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17923 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10809

Test results coming soon (I hope)...

Details

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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).

boegelbot · 2023-05-18T20:01:02Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (3 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/boegelbot/9e0c020c5eb4d31f7049168726085482 for a full test report.

verdurin · 2023-05-22T09:48:27Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-05-22T09:52:08Z

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

PR test command 'EB_PR=17923 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_17923 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2641

Test results coming soon (I hope)...

Details

- notification for comment with ID 1556904248 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).

verdurin · 2023-05-22T09:52:18Z

Test report by @verdurin
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
easybuild-c7.novalocal - Linux CentOS Linux 7.9.2009, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/verdurin/bddbb5c77efa5e1078348a22c716c3e5 for a full test report.

boegelbot · 2023-05-22T09:52:57Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 3 (3 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/boegelbot/d83086afcf8582915d3ff3bd676a1c66 for a full test report.

verdurin · 2023-05-22T13:16:08Z

Here's the build error:

+ echo 'Downloading htslib ...'
Downloading htslib ...
+ '[' '!' -e /tmp/boegelbot/alleleCount/4.2.1/GCC-11.3.0/alleleCount-4.2.1/install_tmp/htslibGet.success ']'
+ cd /tmp/boegelbot/alleleCount/4.2.1/GCC-11.3.0/alleleCount-4.2.1/install_tmp
+ wget https://github.com/samtools/htslib/releases/download/1.11/htslib-1.11.tar.bz2
build/opt-build.sh: line 86: wget: command not found

ItIsI-Orient · 2023-05-23T13:44:44Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-05-23T13:47:08Z

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

PR test command 'EB_PR=17923 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_17923 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2652

Test results coming soon (I hope)...

Details

- notification for comment with ID 1559402681 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).

boegelbot · 2023-05-23T13:47:52Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 3 (3 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/boegelbot/c9ae7413905282b5844abf21e7415625 for a full test report.

boegel · 2023-05-23T17:03:03Z

@ItIsI-Orient Looks like the Perl modules are being installed in a deeper directory?

[boegelbot@jsczen2l1 ~]$ ls /project/def-maintainers/boegelbot/Rocky8/zen2/software/alleleCount/4.2.1-GCC-11.3.0/lib/perl5
5.34.1  Sanger  site_perl  x86_64-linux-thread-multi

[boegelbot@jsczen2l1 ~]$ ls /project/def-maintainers/boegelbot/Rocky8/zen2/software/alleleCount/4.2.1-GCC-11.3.0/lib/perl5/site_perl/5.34.1
Const  Devel  Pod  x86_64-linux-thread-multi

ItIsI-Orient · 2023-06-06T15:03:34Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-06-06T15:12:09Z

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

PR test command 'EB_PR=17923 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_17923 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2730

Test results coming soon (I hope)...

Details

- notification for comment with ID 1578937820 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).

boegelbot · 2023-06-06T15:16:01Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (3 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/boegelbot/d11bb1623a5732600ad91e1ec2ae07f3 for a full test report.

boegel · 2023-06-20T13:28:20Z

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
node3143.skitty.os - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/boegel/8ca679ce77814ffcff48c96fccbe4436 for a full test report.

boegel · 2023-06-20T20:43:23Z

@boegelbot please test @ generoso

boegelbot · 2023-06-20T20:45:09Z

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

PR test command 'EB_PR=17923 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17923 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 11039

Test results coming soon (I hope)...

Details

- notification for comment with ID 1599467815 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).

boegelbot · 2023-06-20T20:50:18Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (3 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/boegelbot/ed33b7c9ad382ad0eb64fc28da7d9a84 for a full test report.

…d in alleleCount easyconfig

boegel · 2023-06-21T15:09:06Z

@boegelbot please test @ generoso

boegelbot · 2023-06-21T15:10:12Z

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

PR test command 'EB_PR=17923 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17923 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 11063

Test results coming soon (I hope)...

Details

- notification for comment with ID 1601020665 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).

boegelbot · 2023-06-21T15:15:04Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (3 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/boegelbot/293e3e18ee25caa280ca00386c204439 for a full test report.

boegel

lgtm

boegel · 2023-06-21T15:24:04Z

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
node3143.skitty.os - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/boegel/c387f0e26ba7ea91ea50741d1e74980a for a full test report.

boegel · 2023-06-21T15:51:32Z

Going in, thanks @ItIsI-Orient!

adding easyconfigs: alleleCount-4.2.1-GCC-11.3.0.eb, ASCAT-3.1.2-foss…

4349ee0

…-2022a-R-4.2.1.eb, alleleIntegrator-0.8.8-foss-2022a-R-4.2.1.eb

ItIsI-Orient added new update labels May 18, 2023

ItIsI-Orient changed the title ~~{bio}[foss/2022a] alleleCount v4.2.1, ASCAT v3.1.2, alleleIntegrator v0.8.8~~ {bio}[GCC/11.3.0,foss/2022a] alleleCount v4.2.1, ASCAT v3.1.2, alleleIntegrator v0.8.8 May 18, 2023

ItIsI-Orient mentioned this pull request May 18, 2023

alleleIntegrator vscentrum/vsc-software-stack#77

Closed

5 tasks

verdurin reviewed May 19, 2023

View reviewed changes

Comment thread easybuild/easyconfigs/a/alleleCount/alleleCount-4.2.1-GCC-11.3.0.eb

boegel requested changes May 23, 2023

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Comment thread easybuild/easyconfigs/a/alleleCount/alleleCount-4.2.1-GCC-11.3.0.eb Outdated

Avoided using the setup.sh script

59cd469

boegel requested changes May 31, 2023

View reviewed changes

Comment thread easybuild/easyconfigs/a/alleleCount/alleleCount-4.2.1-GCC-11.3.0.eb Outdated

Added workaround for jsc-zen2

2ff125a

boegel added this to the 4.x milestone Jun 20, 2023

fix perl shebang for alleleCounter.pl + add extra sanity check comman…

5c06b15

…d in alleleCount easyconfig

boegel approved these changes Jun 21, 2023

View reviewed changes

boegel modified the milestones: 4.x, next release (4.7.3?) Jun 21, 2023

boegel merged commit 15219a8 into easybuilders:develop Jun 21, 2023

Conversation

ItIsI-Orient commented May 18, 2023

Uh oh!

ItIsI-Orient commented May 18, 2023

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boegelbot commented May 18, 2023

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ItIsI-Orient commented Jun 6, 2023

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