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? Traceback (most recent call last): File "/home/galaxy/galaxy-dist/tools/stats/column_maker.py", line 7, in <module> from galaxy.tools import validation File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 15, in <module> from galaxy import util, jobs, model File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 4, in <module> from galaxy import util, model File "/home/galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line 13, in <module> import galaxy.datatypes.registry File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line 6, in <module> import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo, binary, assembly, ngsindex, wsf File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/data.py", line 7, in <module> import metadata File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py", line 5, in <module> from galaxy.web import form_builder File "/home/galaxy/galaxy-dist/lib/galaxy/web/__init__.py", line 5, in <module> from framework import expose, json, json_pretty, require_login, require_admin, url_for, error, form, FormBuilder, expose_api File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py", line 18, in <module> import helpers File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/__init__.py", line 4, in <module> from webhelpers import * File "/home/galaxy/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg/webhelpers/__init__.py", line 1, in <module> from webhelpers.rails import * File "/home/galaxy/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg/webhelpers/rails/__init__.py", line 9, in <module> from text import * File "/home/galaxy/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg/webhelpers/rails/text.py", line 10, in <module> import webhelpers.textile as textile File "/home/galaxy/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg/webhelpers/textile.py", line 241, in <module> import tidy File "/usr/lib/pymodules/python2.6/tidy/__init__.py", line 43, in <module> from tidy.lib import parse, parseString File "/usr/lib/pymodules/python2.6/tidy/lib.py", line 24, in <module> os.environ['PATH'] = "%s%s%s" % (packagedir, os.pathsep, os.environ['PATH']) File "/usr/lib/python2.6/UserDict.py", line 22, in __getitem__ raise KeyError(key) KeyError: 'PATH' Thank you so much again for your help. Oren