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
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to