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