Hi John,
As I specified it in the edit of my first message, I have this error
only if I run groomer with a command line in another xml file
surrounding by other command. When I run groomer alone with the
original xml, it works fine, so no problem with the PYTHONPATH.
But when I use this :
Ahhh - I get it now. Galaxy only adds itself to the PYTHONPATH if it
can infer it is running a Python script (i.e. the command block starts
with python or a Python interpreter is used).
If you are building a tool for the tool shed - it would be best to
setup a tool dependency on the
Thanks!
Actually it's not for the toolshed, for the moment...
But I'm very intereseted by details to install it into a virtualenv.
Thank you.
Julie
2014-07-07 16:16 GMT+02:00 John Chilton jmchil...@gmail.com:
Ahhh - I get it now. Galaxy only adds itself to the PYTHONPATH if it
can infer it is
If your tool defines a package requirement like:
requirements
requirement type=package version=1.0.0galaxy-sequence-utils/requirement
/requirements
And your tool_dependency_dir setting universe_wsgi.ini is something
like /data/galaxy_deps - then you should be able to create a file
Hello Julie,
This is odd - sorry.
I might be worth uninstalling and re-installing this in the tool
shed admin options - in particular ensure you install tool
dependencies and that this installation process succeeds.
Otherwise - it might be worth trying to put some debug statements
in the
