Hi Peter,
Yes, if you wanted to create a ticket in bitbucket for this patch that
would be great. It is the best way to help us to keep track/prioritize.
Please just submit, but don't change status from "new" or assign to
anyone in particular. Do feel free to note whether a ticket is intended
as a bug (fix), enhancement, or proposal.
Ideally, all submitted patches (from anyone) should go there. Then, the
creator can email galaxy-dev with the link and a description to let our
team and the other users know about it.
http://bitbucket.org/galaxy/galaxy-central/issues
When a tool is added to the Tool Shed, an email to galaxy-dev is also
welcomed, to let the community know about what's new or to gather
feedback. We encourage tool developers to submit first to the Tool Shed
any stand-alone tools, then request if the tool might be appropriate for
the core build (if they want and use is broad enough) as an enhancement.
http://galaxyproject.org/Tool%20Shed
To remind others (readers of this email), bitbucket is not intended to
replace the mailing lists for suspected bugs/bug reports, questions, or
general discussion.
http://galaxyproject.org/Support
The galaxy-dev list has become a very active community and we really
appreciate all of your input Peter!
Take care,
Jen
Galaxy team
On 8/4/11 2:51 AM, Peter Cock wrote:
On Fri, Jul 29, 2011 at 2:22 PM, Peter Cock<p.j.a.c...@googlemail.com> wrote:
Hi all,
I've run into some file permissions problems as part of using the same
mapped directory on both the Galaxy server and our cluster. In the
process I wrote the following patch which fixes the following bug -
where Galaxy seems to leave the job in the pending state:
galaxy.jobs INFO 2011-07-29 14:06:46,170 job 30 dispatched
galaxy.jobs.runners.drmaa ERROR 2011-07-29 14:06:46,582 Uncaught
exception queueing job
Traceback (most recent call last):
File "/data/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py",
line 114, in run_next
self.queue_job( obj )
File "/data/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py",
line 164, in queue_job
os.chmod( jt.remoteCommand, 0750 )
OSError: [Errno 1] Operation not permitted:
'/data/galaxy/galaxy-central/database/pbs/galaxy_30.sh'
The jobs was left stuck in the grey pending state. It looks like this
exception should have been caught and the job put into an error
state as in this patch:
https://bitbucket.org/peterjc/galaxy-central/changeset/c5fa48633c0b
This is currently the one and only change on this branch:
https://bitbucket.org/peterjc/galaxy-central/src/job_scripts
Please could this be reviewed and applied to the trunk.
Thanks,
Peter
Should I file a bug with this patch?
Peter
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Jennifer Jackson
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