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 <dcsh...@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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