After upgrading from the October 2014 release to 15.03 we started
experiencing job failures for one of our custom tools, which I eventually
tracked down to PYTHONPATH now being set in the job environment to
$GALAXY_HOME/lib. The dependencies for this tool are installed in a
virtualenv that is activated by the tool dependency package's env.sh. It
looks like one of the scripts in this virtualenv attempts to use setuptools
to find its dependencies, but because of the PYTHONPATH setting ends up in
Galaxy's $GALAXY_HOME/lib/pkg_resources.py:

```
Traceback (most recent call last):
  File
"/mnt/scdata/scdata_03/galaxy/containers/galaxy-qa/export/tool_deps/yapp_env/new/venv/bin/sequencing_quality_report.py",
line 8, in <module>
    from pkg_resources import load_entry_point
  File
"/mnt/scdata/scdata_03/galaxy/containers/galaxy-qa/stable/lib/pkg_resources.py",
line 2603, in <module>
    working_set.require(__requires__)
  File
"/mnt/scdata/scdata_03/galaxy/containers/galaxy-qa/stable/lib/pkg_resources.py",
line 666, in require
    needed = self.resolve(parse_requirements(requirements))
  File
"/mnt/scdata/scdata_03/galaxy/containers/galaxy-qa/stable/lib/pkg_resources.py",
line 565, in resolve
    raise DistributionNotFound(req)  # XXX put more info here
pkg_resources.DistributionNotFound: pytz>=2011k
```

I worked around this issue by prepending the virtualenv's
lib/python2.7/site-packages directory to PYTHONPATH in the tool dependency
package's env.sh, but I'm a bit confused why this is now necessary. Can
anyone shed some light on what changed?


Cheers,

Brian

-- 
Brian Claywell | programmer/analyst
Matsen Group   | http://matsen.fredhutch.org <http://matsen.fhcrc.org/>
Fred Hutchinson Cancer Research Center
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