Hi,

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 ?

Best,
Wolfgang

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

Reply via email to