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 ___________________________________________________________ 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/
