Thanks for the tip Eric. I was able to figure it out. The key to this, was you suggested was permission issue. I had to modify sudoers so tty was not required. This will allow scripts to change ownership to the correct user so SGE can submit them. Thanks! -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences System Administrator, HPC Cluster Office of Information Technology http://hpc.oit.uci.edu/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne@uci.edu On Mon, Feb 3, 2014 at 9:57 AM, Eric Rasche <rasche.eric@yandex.ru> wrote:

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1

Looks like a permission issue. Is your FTP server set to use the same user/group as galaxy?

For reference: my proftpd is configured to use LDAP user information, but then it forces the user/group id of uploaded files to be that of galaxy

# Force those numbers even if LDAP finds a valid UID/GID LDAPDefaultUID {galaxy's UID} LDAPDefaultGID {galaxy group GID}

Hope that helps

On 02/03/2014 11:23 AM, Adam Brenner wrote:

...

Anyone have any ideas on this?

Thanks, -Adam

-- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences

System Administrator, HPC Cluster Office of Information Technology http://hpc.oit.uci.edu/

University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne@uci.edu

On Thu, Jan 30, 2014 at 2:33 PM, Adam Brenner <aebrenne@uci.edu> wrote:

...

Howdy,

I am having trouble uploading data on our local instance of Galaxy here. The method is via FTP and here is the error I am seeing in the logs:

galaxy.jobs.runners DEBUG 2014-01-30 14:29:31,987 execution of external set_meta for job 1367 finished galaxy.jobs DEBUG 2014-01-30 14:29:32,016 (1367) Changing ownership of working directory with: /usr/bin/sudo -E scripts/external_chown_script.py /som/galaxy/database/job_working_directory/001/1367 root 0 galaxy.jobs ERROR 2014-01-30 14:29:32,058 (1367) Failed to change ownership of /som/galaxy/database/job_working_directory/001/1367, failing Traceback (most recent call last): File "/data/apps/galaxy/dist/lib/galaxy/jobs/__init__.py", line 870, in finish self.reclaim_ownership() File "/data/apps/galaxy/dist/lib/galaxy/jobs/__init__.py", line 1316, in reclaim_ownership self._change_ownership( self.galaxy_system_pwent[0], str( self.galaxy_system_pwent[3] ) ) File "/data/apps/galaxy/dist/lib/galaxy/jobs/__init__.py", line 1302, in _change_ownership assert p.returncode == 0 AssertionError

Any idea on how to fix the issue? Thanks, -Adam

-- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences

System Administrator, HPC Cluster Office of Information Technology http://hpc.oit.uci.edu/

University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne@uci.edu

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- -- Eric Rasche Programmer II Center for Phage Technology Texas A&M University College Station, TX 77843 404-692-2048 esr@tamu.edu rasche.eric@yandex.ru -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux)

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