{bio}[foss/2021b] GUSH v2020-09-28 by deniskristak · Pull Request #16905 · easybuilders/easybuild-easyconfigs

deniskristak · 2022-12-15T09:34:12Z

No description provided.

code-style change + deprecation param err

smoors · 2022-12-19T17:59:33Z

@boegelbot: please test @ generoso

boegelbot · 2022-12-19T18:00:10Z

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

PR test command 'EB_PR=16905 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_16905 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 9836

Test results coming soon (I hope)...

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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 · 2022-12-19T18:02:33Z

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/a04ca234bafbb37c94240b153e9613b1 for a full test report.

smoors · 2022-12-19T18:09:40Z

@boegelbot please test @ jsc-zen2

boegelbot · 2022-12-19T18:12:13Z

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

PR test command 'EB_PR=16905 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_16905 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 1927

Test results coming soon (I hope)...

Details

- notification for comment with ID 1358048659 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 · 2022-12-19T18:14:53Z

Test report by @boegelbot
FAILED
Build succeeded for 2 out of 3 (1 easyconfigs in total)
jsczen2g1.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/49b691485c1e852acefecd7b72a7d2ee for a full test report.

smoors · 2022-12-19T18:37:16Z

@deniskristak the sanity_check_commands downloads stuff with wget.
is there another command that we can use instead that doesn't download?

./gushr.py -t example/augustus.gtf -b example/RNAseq.bam -g example/genome.fa -o utrs exited with code 1 (output: ./download_rnaseq.sh: line 1: wget: command not found

boegel · 2023-01-03T11:13:52Z

@deniskristak the sanity_check_commands downloads stuff with wget. is there another command that we can use instead that doesn't download?
./gushr.py -t example/augustus.gtf -b example/RNAseq.bam -g example/genome.fa -o utrs exited with code 1 (output: ./download_rnaseq.sh: line 1: wget: command not found

One option here could be to pre-download whatever is being pulled in via sources, and then seeding that into the right place when running the sanity check command...

smoors · 2023-01-08T17:37:15Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-01-08T17:42:10Z

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

PR test command 'EB_PR=16905 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_16905 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2020

Test results coming soon (I hope)...

Details

- notification for comment with ID 1374888340 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 · 2023-01-08T17:43:29Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 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/1eebaaec8d347e14f92d279f947a0163 for a full test report.

smoors

lgtm

smoors · 2023-01-09T09:03:17Z

Going in, thanks @deniskristak!

deniskristak and others added 2 commits December 15, 2022 10:33

adding easyconfigs: GUSHR-2020-09-28-foss-2021b.eb

7bc7b4f

Update GUSHR-2020-09-28-foss-2021b.eb

4516467

code-style change + deprecation param err

deniskristak mentioned this pull request Dec 15, 2022

{bio}[foss/2021b] finder v1.1.0 #16910

Merged

SebastianAchilles added this to the 4.x milestone Dec 15, 2022

smoors added the new label Dec 19, 2022

use single rather than double quotes

7f5f406

boegel changed the title ~~adding easyconfigs: GUSHR-2020-09-28-foss-2021b.eb~~ {bio}[foss/2021b] GUSH v2020-09-28 Jan 2, 2023

deniskristak and others added 4 commits January 4, 2023 15:19

updating GUSHR sanity check

162f93b

updating GUSHR sanity check

a87a5c9

updating GUSHR sR java version

1959966

use single rather than double quotes

8a685fe

smoors approved these changes Jan 9, 2023

View reviewed changes

smoors modified the milestones: 4.x, release after 4.7.0 Jan 9, 2023

smoors merged commit c40b0a1 into easybuilders:develop Jan 9, 2023

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deniskristak commented Dec 15, 2022

Uh oh!

smoors commented Dec 19, 2022

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boegelbot commented Dec 19, 2022

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boegelbot commented Dec 19, 2022

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smoors commented Dec 19, 2022

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boegelbot commented Dec 19, 2022

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boegelbot commented Dec 19, 2022

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smoors commented Dec 19, 2022

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boegel commented Jan 3, 2023

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smoors commented Jan 8, 2023

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smoors commented Jan 9, 2023

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