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