Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[16.07] Fix metadata collection on workdir outputs for Pulsar. #2721

Merged

Conversation

Projects
None yet
4 participants
@jmchilton
Copy link
Member

commented Aug 3, 2016

a2e3140 which gave tool's clean working directories made the function get_workdir_outputs a big sloppy. Pulsar would send it the actual remote working directory for jobs and Galaxy would send it the job directory (expecting it to append 'working').

Fixup metadata collection on workdir outputs for Pulsar.
a2e3140 which gave tool's clean working directories made the function get_workdir_outputs a big sloppy. Pulsar would send it the actual remote working directory for jobs and Galaxy would send it the job directory (expecting it to append 'working').

@jmchilton jmchilton added this to the 16.07 milestone Aug 3, 2016

@natefoo

This comment has been minimized.

Copy link
Member

commented Aug 3, 2016

👍 if tests pass, and thank you!

@natefoo

This comment has been minimized.

Copy link
Member

commented Aug 3, 2016

I should add, 👍 to applying this to 16.04 as well, since that should be the first release it broke in.

@jmchilton

This comment has been minimized.

Copy link
Member Author

commented Aug 3, 2016

I retain the belief that only main uses the undocumented remote metadata options - so I think it would be a waste to backport this to 16.04.

@natefoo

This comment has been minimized.

Copy link
Member

commented Aug 3, 2016

Ok, I won't put up a fight.

@galaxybot

This comment has been minimized.

Copy link

commented Aug 3, 2016

@jmchilton's PR has reached the required number of votes for merging.

@dannon dannon merged commit 82430c0 into galaxyproject:release_16.07 Aug 3, 2016

4 checks passed

api test Build finished. 224 tests run, 0 skipped, 0 failed.
Details
continuous-integration/travis-ci/pr The Travis CI build passed
Details
framework test Build finished. 111 tests run, 0 skipped, 0 failed.
Details
toolshed test Build finished. 582 tests run, 0 skipped, 0 failed.
Details
@natefoo

This comment has been minimized.

Copy link
Member

commented Aug 4, 2016

This fixed the working/working/ problem on setting metadata on tophat's align_summary.txt. Setting metadata on accepted_hits.bam still fails with "No such file or directory" reported by set_metadata() but the path to accepted_hits.bam is correct (and the file exists) so this seems to be a different issue. Perhaps just NFS attribute caching if that bam file is created just moments prior to running set_metdata()

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
You can’t perform that action at this time.