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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