I am not sure whether I am diagnosing this problem approximately right or not, but it seems that with the latest release of Galaxy (stable branch, latest_2015.01.13) enviroment variables set in a tool-dependency's env.sh file and sourced before a job run are now leaking through to

./scripts/set_metadata.py called after the tool run finishes.

In my specific case, the sourced env.sh adds a python 3 virtualenv directory to PATH, which then causes set_metadata.py to fail with:

  File "./scripts/set_metadata.py", line 130
    except Exception, e:
SyntaxError: invalid syntax

because that (amazingly enough :)) seems to be the first line not compatible with Python 3.

I have not seen this error before (I believe not with latest_2014.10.06) so I guess my question is: has the way that set_metadata.py is called been changed recently and would you consider the current behavior a bug or is this expected and ok ?


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