Skip to content

{bio}[foss/2020a] OPERA-MS v0.9.0#11410

Merged
boegel merged 4 commits intoeasybuilders:developfrom
zarybnicky:20200930151851_new_pr_OPERA-MS090
Oct 15, 2020
Merged

{bio}[foss/2020a] OPERA-MS v0.9.0#11410
boegel merged 4 commits intoeasybuilders:developfrom
zarybnicky:20200930151851_new_pr_OPERA-MS090

Conversation

@zarybnicky
Copy link
Copy Markdown
Contributor

@zarybnicky zarybnicky commented Sep 30, 2020

(created using eb --new-pr)

@zarybnicky
Copy link
Copy Markdown
Contributor Author

zarybnicky commented Sep 30, 2020 •
edited
Loading

Instead of e.g. perl <install dir>/OPERA-MS.pl --help as per instructions, you can use OPERA-MS --help, a wrapper script.

boegel
boegel requested changes Sep 30, 2020
View reviewed changes
Comment thread easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-foss-2020a.eb
Comment thread easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-foss-2020a.eb Outdated
Comment thread easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-foss-2020a.eb Outdated
@boegel boegel added the new label Sep 30, 2020
@boegel boegel added this to the 4.x milestone Sep 30, 2020
@smoors
Copy link
Copy Markdown
Contributor

smoors commented Oct 1, 2020

@boegelbot please test @ generoso

@boegelbot
Copy link
Copy Markdown
Collaborator

boegelbot commented Oct 1, 2020

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

PR test command 'EB_PR=11410 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_11410 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 7997

Test results coming soon (I hope)...

Details

- notification for comment with ID 702319422 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).

@smoors
Copy link
Copy Markdown
Contributor

smoors commented Oct 1, 2020

Test report by @smoors
SUCCESS
Build succeeded for 2 out of 2 (1 easyconfigs in this PR)
node375.hydra.os - Linux centos linux 7.7.1908, x86_64, Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz (skylake_avx512), Python 2.7.5
See https://gist.github.com/8a2f083404f99ff68a9dc847d074571d for a full test report.

@boegelbot
Copy link
Copy Markdown
Collaborator

boegelbot commented Oct 1, 2020

Test report by @boegelbot
FAILED
Build succeeded for 1 out of 2 (1 easyconfigs in this PR)
generoso-x-3 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/534623a3520afdc5782e6ab9ecc41210 for a full test report.

boegel
boegel requested changes Oct 5, 2020
View reviewed changes
Copy link
Copy Markdown
Member

@boegel boegel left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@zarybnicky The test command you're running via postinstallcmds requires python to be available.

There's no python command available on the CentOS8 test system used in the failing test report, which explains the failure.
This is included in the gap_filling.err output file:

python /software/OPERA-MS/0.9.0-foss-2020a//OPERA-LG/bin//Remap.py /tmp/eb-hi1cjvya/intermediate_files/opera_long_read/GAPFILLING/TILLING/first_tilling.paf /tmp/eb-hi1cjvya/intermediate_files/opera_long_read/GAPFILLING/TILLING/consensus.fa /tmp/eb-hi1cjvya/intermediate_files/opera_long_read/GAPFILLING/TILLING/first_tilling_contig.fa > /tmp/eb-hi1cjvya/intermediate_files/opera_long_read/GAPFILLING/TILLING/tilling_1_remap.out
sh: python: command not found

So Python should be included as a dependency (probably runtime, since the OPERA-MS installation includes Python scripts?

@zarybnicky
Copy link
Copy Markdown
Contributor Author

zarybnicky commented Oct 5, 2020

@boegel Ah, thanks for that. I've seen that log and wanted to ask you today for that log file, as the gist only says Please see /tmp/eb-zsnq4q7g/intermediate_files/opera_long_read/GAPFILLING/gap_filling.err for details.

@boegel
Copy link
Copy Markdown
Member

boegel commented Oct 14, 2020

@boegelbot please test @ generoso

@boegelbot
Copy link
Copy Markdown
Collaborator

boegelbot commented Oct 14, 2020

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

PR test command 'EB_PR=11410 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_11410 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 8083

Test results coming soon (I hope)...

Details

- notification for comment with ID 708611044 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
Copy link
Copy Markdown
Collaborator

boegelbot commented Oct 14, 2020

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
generoso-x-2 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/60e6b2b00e6da461e130c3cc5a9f86be for a full test report.

@boegel
Copy link
Copy Markdown
Member

boegel commented Oct 14, 2020

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3401.kirlia.os - Linux centos linux 7.8.2003, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz (cascadelake), Python 2.7.5
See https://gist.github.com/88b9966228dacd6777d65933029992a0 for a full test report.

@boegel
Copy link
Copy Markdown
Member

boegel commented Oct 14, 2020

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (1 easyconfigs in this PR)
node3108.skitty.os - Linux centos linux 7.8.2003, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/ed3a51111250c22fad5aafeef94bbb6d for a full test report.

@easybuilders easybuilders deleted a comment from boegelbot Oct 14, 2020
@boegel
Copy link
Copy Markdown
Member

boegel commented Oct 15, 2020

Going in, thanks @zarybnicky!

@boegel boegel merged commit 06ddd55 into easybuilders:develop Oct 15, 2020
@zarybnicky zarybnicky deleted the 20200930151851_new_pr_OPERA-MS090 branch October 15, 2020 09:48
@boegel boegel mentioned this pull request Oct 15, 2020
Closed
@boegel boegel modified the milestones: 4.x, next release (4.3.1) Oct 16, 2020
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@boegel boegel boegel approved these changes

Assignees

No one assigned

Labels

new

Projects

None yet

Milestone

4.3.1

Development

Successfully merging this pull request may close these issues.

4 participants

@zarybnicky @smoors @boegelbot @boegel