Hi,
I am trying to setup my galaxy system to allow jobs to be submitted as the real user, since people want to keep an eye on their job on the cluster sometimes and they have no ideas which ones are theirs. I tried the approach on the wiki here: http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster?highlight=%28 submit%29%7C%28jobs%29%7C%28as%29%7C%28user%29#Submitting_Jobs_as_the_Real_U ser but unfortunately, the CHOWN command is not allowed, not even as a sudo user. Probably has to do with the fact that we run our cluster from an isilon system, which I assume is pretty typical. The job was actually successfully submitted as the intended user, so that part works, but if we can just get it to work without having to rely on chown that would be awesome. Can someone point me in the right direction? Here's the error. galaxy.jobs.runners.local DEBUG 2013-02-19 19:35:31,524 execution of external set_meta for job 148 finished galaxy.jobs DEBUG 2013-02-19 19:35:31,576 (148) Changing ownership of working directory with: /usr/bin/sudo -E scripts/external_chown_script.py /mnt/ngs/analysis/svcgalaxy/galaxy-test/database/job_working_directory/000/1 48 svcgalaxy 10000 galaxy.jobs ERROR 2013-02-19 19:35:31,653 (148) Failed to change ownership of /mnt/ngs/analysis/svcgalaxy/galaxy-test/database/job_working_directory/000/1 48, failing Traceback (most recent call last): File "/mnt/ngs/analysis/svcgalaxy/galaxy-test/lib/galaxy/jobs/__init__.py", line 343, in finish self.reclaim_ownership() File "/mnt/ngs/analysis/svcgalaxy/galaxy-test/lib/galaxy/jobs/__init__.py", line 916, in reclaim_ownership self._change_ownership( self.galaxy_system_pwent[0], str( self.galaxy_system_pwent[3] ) ) File "/mnt/ngs/analysis/svcgalaxy/galaxy-test/lib/galaxy/jobs/__init__.py", line 902, in _change_ownership assert p.returncode == 0 AssertionError galaxy.jobs DEBUG 2013-02-19 19:35:31,722 fail(): Moved /mnt/ngs/analysis/svcgalaxy/galaxy-test/database/job_working_directory/000/1 48/galaxy_dataset_332.dat to /mnt/ngs/analysis/svcgalaxy/galaxy-test/database/files/000/dataset_332.dat galaxy.datatypes.metadata DEBUG 2013-02-19 19:35:31,924 Cleaning up external metadata files Thanks Thon
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