Jobs run as the condor user? That is surprising - Galaxy isn't running as the condor user is it? Is your intention to have the jobs run as the 'galaxy' user or to run as the LDAP authenticated end-user submitting the job? If it is to run as the Galaxy user - I think it would be best to have condor reconfigured to run jobs as the submitting user (in this case galaxy) - at most institutions that is the way these things are usually configured. If you would like to run the jobs as the actual LDAP authenticated user - that is going to require a somewhat significant development effort. In that case I would look at the drmaa runner and what it is doing to run jobs as the actual user and try to do similar things in the condor runner - I don't think it would be a couple lines of hacking. condor has a DRMAA interface - I have never heard of it being used with Galaxy but that might be something worth trying as well. If you can get that to work - you should be able to use the drmaa run as real user mode. -John On Wed, Aug 6, 2014 at 4:40 PM, Shrum, Donald C <DCShrum@admin.fsu.edu> wrote:

Our galaxy server has an apache front end with ldap authentication.

I've added a condor destination... <plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner"/> <destination id="condor" runner="condor"/>

There are some tools I'd like to point to condor but it appears all the jobs will be sent as the user condor.

Is there an existing fix that will submit jobs to our condor cluster as the logged in user?

If not could someone give me a small pointer for a hack fix? Something along the lines of:

galaxy-dist/lib/galaxy/jobs/runners/util/condor/__init__.py

line 71: submit = Popen(('condor_submit', submit_file), stdout=PIPE, stderr=STDOUT)

Could be changed to sudo -u xxx -c condor_submit...

Thanks all, Don FSU Research Computing Center

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