{bio}[GCC/11.3.0] CD-HIT v4.8.1, GenomeTools v1.6.2, Kent_tools v442, ... #17249

smoors · 2023-02-02T18:48:03Z

(created using eb --new-pr)

depends on #17245

…-11.3.0.eb, Kent_tools-442-GCC-11.3.0.eb, LTR_retriever-2.9.0-foss-2022a.eb, RECON-1.08-GCC-11.3.0.eb, RepeatModeler-2.0.4-foss-2022a.eb, RepeatScout-1.0.6-GCC-11.3.0.eb, TWL-NINJA-0.98-cluster_only-GCC-11.3.0.eb and patches: Kent_tools-442_openssl.patch

smoors · 2023-02-03T07:02:32Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-02-03T07:07:09Z

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

PR test command 'EB_PR=17249 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_17249 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2151

Test results coming soon (I hope)...

Details

- notification for comment with ID 1415173821 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 · 2023-02-03T07:11:26Z

Test report by @boegelbot
FAILED
Build succeeded for 7 out of 8 (8 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/f7a4efba2ec0f863ed5ccb95a8b85caa for a full test report.

smoors · 2023-02-03T08:32:57Z

@boegelbot: please test @ generoso

boegelbot · 2023-02-03T08:35:09Z

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

PR test command 'EB_PR=17249 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17249 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10106

Test results coming soon (I hope)...

Details

- notification for comment with ID 1415346427 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 · 2023-02-03T08:42:36Z

Test report by @boegelbot
SUCCESS
Build succeeded for 8 out of 8 (8 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/dd4cb716e9b1c9162f9cb74962828895 for a full test report.

branfosj · 2023-02-03T08:58:49Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-02-03T09:02:10Z

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

PR test command 'EB_PR=17249 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_17249 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2154

Test results coming soon (I hope)...

Details

- notification for comment with ID 1415397803 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 · 2023-02-03T09:06:00Z

Test report by @boegelbot
FAILED
Build succeeded for 7 out of 8 (8 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/fc8bbcd34896e039d6fef457cf696c4c for a full test report.

branfosj · 2023-02-03T09:48:51Z

Test report by @branfosj
SUCCESS
Build succeeded for 14 out of 14 (8 easyconfigs in total)
bear-pg0105u03a.bear.cluster - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/14ab0b6eeec8652e105412fab2d2cc0c for a full test report.

failure on jsc-zen2

branfosj · 2023-02-03T09:56:43Z

Test report by @branfosj
FAILED
Build succeeded for 15 out of 17 (8 easyconfigs in total)
bear-pg0211u03a.bear.cluster - Linux Ubuntu 20.04.2 LTS (Focal Fossa), x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.8.5
See https://gist.github.com/4ee08fe4b11c285518db4c1fc65a1c2b for a full test report.

easybuild/easyconfigs/k/Kent_tools/Kent_tools-442-GCC-11.3.0.eb

easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.4-foss-2022a.eb

smoors · 2023-02-04T15:45:25Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-02-04T15:47:08Z

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

PR test command 'EB_PR=17249 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_17249 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2160

Test results coming soon (I hope)...

Details

- notification for comment with ID 1416785571 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 · 2023-02-04T15:51:05Z

Test report by @boegelbot
SUCCESS
Build succeeded for 8 out of 8 (8 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/7817f7c1973d6747c332f1b64dc0ac37 for a full test report.

changes done

branfosj · 2023-02-05T08:37:09Z

Test report by @branfosj
SUCCESS
Build succeeded for 8 out of 8 (8 easyconfigs in total)
bear-pg0105u03a.bear.cluster - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/755e9dddcb1df7324ca918ccfa1e5a05 for a full test report.

branfosj · 2023-02-05T08:38:23Z

Test report by @branfosj
SUCCESS
Build succeeded for 8 out of 8 (8 easyconfigs in total)
bear-pg0211u03a.bear.cluster - Linux Ubuntu 20.04.2 LTS (Focal Fossa), x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.8.5
See https://gist.github.com/0c4c1a7a73159aed9be78420f519e870 for a full test report.

branfosj · 2023-02-05T08:38:32Z

Going in, thanks @smoors!

smoors added the update label Feb 2, 2023

update sanity check command for RepeatModeler

aba58e6

branfosj previously approved these changes Feb 3, 2023

View reviewed changes

branfosj previously requested changes Feb 3, 2023

View reviewed changes

easybuild/easyconfigs/k/Kent_tools/Kent_tools-442-GCC-11.3.0.eb Show resolved Hide resolved

easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.4-foss-2022a.eb Show resolved Hide resolved

branfosj mentioned this pull request Feb 3, 2023

remove use of rysnc in building Kent_tools #17252

Merged

Samuel Moors added 2 commits February 4, 2023 11:02

replace rsync with cp for Kent_tools

f83c568

fix perl shebang for RepeatModeler executable

12d5c58

smoors mentioned this pull request Feb 4, 2023

automatically detect shebangs with hardcoded paths boegel/boegelbot#24

Open

branfosj added this to the next release (4.7.1?) milestone Feb 5, 2023

branfosj approved these changes Feb 5, 2023

View reviewed changes

branfosj merged commit 79526e2 into easybuilders:develop Feb 5, 2023

smoors deleted the 20230202194758_new_pr_CD-HIT481 branch January 21, 2026 09:24

{bio}[GCC/11.3.0] CD-HIT v4.8.1, GenomeTools v1.6.2, Kent_tools v442, ... #17249

{bio}[GCC/11.3.0] CD-HIT v4.8.1, GenomeTools v1.6.2, Kent_tools v442, ... #17249

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smoors commented Feb 2, 2023 •

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