Dear Galaxy mailing list,

We ran into the same issue described in this post: http://dev.list.galaxyproject.org/markupsafe-module-conflicts-tc4656214.html
The exact error message we are getting, with a few different tools is:

/Galaxy/galaxy_dist/lib/galaxy/__init__.py:79: UserWarning: Module markupsafe was already imported from /usr/lib64/python2.6/site-packages/markupsafe/__init__.pyc, but /Galaxy/galaxy_dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg is being added to sys.path
self.check_version_conflict()

From the solution given in the above-mentioned post, I guess we would have to run Galaxy inside virtualenv. (Details of the procedure to install virtualenv, are given here: http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer)

However, I am not sure to understand completely how it works.
Can we use our already existing Galaxy instance with virtualenv?  And how can we achieve this?

For the installation of "virtualenv" part, I think we are ok.
It is the next step: how to tell Galaxy to run in this virtualenv, that I am not sure about.

Thank you in advance for your help!


Jean-Francois
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