Okay! I found out what the issue was. I am not sure if this is related to the new Galaxy setup (requiring job_conf.xml) but, I added the following lines to my universe_wsgi.ini, saved, restarted and it worked.
drmaa_external_runjob_script = scripts/drmaa_external_runner.py drmaa_external_killjob_script = scripts/drmaa_external_killer.py external_chown_script = scripts/external_chown_script.py So the bigger question is: Is the current documentation wrong and adding drmaa to the job_conf.xml incorrect? If not, then what I am doing wrong in my file? Thanks, -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebre...@uci.edu On Tue, Apr 23, 2013 at 10:47 AM, Adam Brenner <aebre...@uci.edu> wrote: > Anyone have any ideas as to why its not running? Surely must be a few > users who run Galaxy via a Scheduler using DRMAA... > > My updated job_conf.xml is like so: http://pastebin.com/raw.php?i=QJbay57i > > > Jobs do get submitted to DRMAA, but the scripts are never called to run as > real user. I have DEBUG set to true in universe_wsgi.ini and nothing > regarding errors or debug message are created in paster.log about this. > > -- > Adam Brenner > Computer Science, Undergraduate Student > Donald Bren School of Information and Computer Sciences > > Research Computing Support > Office of Information Technology > http://www.oit.uci.edu/rcs/ > > University of California, Irvine > www.ics.uci.edu/~aebrenne/ > aebre...@uci.edu > > > On Tue, Apr 16, 2013 at 4:55 PM, Adam Brenner <aebre...@uci.edu> wrote: > >> I have the following job_conf.xml file setup for our cluster: >> http://pastebin.com/raw.php?i=0uNhcVJk >> >> When running jobs from my admin account via Galaxy it runs under the same >> user as galaxy is, for testing, this as root. I need for it to run under >> the real user. >> >> The email address / galaxy account I am using to test with does match >> with a user on the cluster -- u...@example.com where user is a valid >> user account with correct permissions to run jobs on our cluster and queue. >> >> I followed the information here: >> http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#Submitting_Jobs_as_the_Real_User >> >> Any ideas as to why galaxy_external* is not being called? The paster.log >> file does not show anything useful regarding calling external scripts. >> >> -- >> Adam Brenner >> Computer Science, Undergraduate Student >> Donald Bren School of Information and Computer Sciences >> >> Research Computing Support >> Office of Information Technology >> http://www.oit.uci.edu/rcs/ >> >> University of California, Irvine >> www.ics.uci.edu/~aebrenne/ >> aebre...@uci.edu >> > >
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