On Wed, Oct 05, 2011 at 01:00:35PM -0500, Oren Livne wrote:
> Dear Nathan,
> 
> We found that condor was running the job as the "nobody" user, which
> had no permissions to the files galaxy created in the database/pbs
> directory. This was fixed by setting
> 
> TRUST_UID_DOMAIN = True
> 
> in the condor config file.
> 
> Now the job runs, but fails immediately because it cannot find the
> PATH environment variable. If I run the generated
> database/pbs/galaxy_<jobID>.sh file manually at the command line, it
> works fine. Do we need any some environment setting in
> galaxy/condor?

You can set the environment by using an "environment = " command in the submit
file or, if appropriate, you can copy your environment to the job by inserting
"getenv = true" in the submit file.

This is described in the condor manual at
http://www.cs.wisc.edu/condor/manual/v7.7/2_5Submitting_Job.html#2516
> Thank you so much again for your help.

You're welcome

Nathan Panike
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