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/ aebre...@uci.edu On Mon, Feb 3, 2014 at 9:57 AM, Eric Rasche <rasche.e...@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/ >> aebre...@uci.edu >> >> >> On Thu, Jan 30, 2014 at 2:33 PM, Adam Brenner <aebre...@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/ >>> aebre...@uci.edu >> ___________________________________________________________ >> 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/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > > - -- > Eric Rasche > Programmer II > Center for Phage Technology > Texas A&M University > College Station, TX 77843 > 404-692-2048 > e...@tamu.edu > rasche.e...@yandex.ru > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v2.0.17 (GNU/Linux) > > iQIcBAEBAgAGBQJS79hyAAoJEMqDXdrsMcpV2tIP/3k218ARn3VIvYlhTT0SRGsP > 8Qgt1w0AgPUSv897MsoS3IQwVqNG4ZJtTPJWgyd+asi0DDPb1lERWSeCXHRr1QSn > gQmT3Q2sW2tM7sx1OINwMqQ34Hly0bOJiN3/ifOxNaqp3LYjqfWmEvHszQUb3OS1 > mS4JGrrAuZC4z38KohLC93FRLRwA+tOtw6Cw35ViFJZ+MnAWXcalew+WdhnCJmUg > jqXqWHLk8+d3K/FKkn0xkSL5UK9MMn4d6g/TBV3UeG0vOIhFzY3r3sxQKEjtT5x6 > /p4qeCAgYWZ8woFQn+mSyrLmYCC5U+jKvtlsuu4la/GhNxFTj9ohppi6SDRn5bsf > I8WDXQS7Hu8qkvVDi0THty0Mbx01/YyYkqfNTWCySEHPUJdwh0WeRW8G5vt374lm > Mq0eyvbQIrjqBDN9XjVdfagXrtC2lcot4Nn3bCcLYNG4DRdNMM+zZmyIa6tKq2l/ > 2TrbLxaFs0AMYpj0p99rFpjYyzWy+IofmsAMmdmZqs39rStetSh+V26dFY1nS6sM > o6cLL5tKBzDuP/gbU3qCLHRryBInUo+FKUxFHUy1FxUJGoAAL02R5eB1OhDozfCr > o2lFeKHfZuKToa5VPS4On5QuywWCSQghoD8LvJNcX9zumwjQz0sUbogPt5x9PDh7 > h9mwsn570ZgbXWZ2FQmM > =0oH0 > -----END PGP SIGNATURE----- > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
