{bio}[foss/2021b] GUSH v2020-09-28

[deniskristak]

No description provided.

[smoors]

@boegelbot: please test @ generoso

[boegelbot]

@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)...

- notification for comment with ID 1358033053 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]

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]

@boegelbot please test @ jsc-zen2

[boegelbot]

@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)...

- 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]

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]

@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]

@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]

@boegelbot please test @ jsc-zen2

[boegelbot]

@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)...

- 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]

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]

Going in, thanks @deniskristak!