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

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