Hi Dannon, We are using Galaxy distribution from February 8, 2013. We didn't have time to update to the April 1st distribution yet. I think the update is planned for next Monday. Is this issue supposed to be solved in the February 8 distribution as well? Or only in the latest (from April 1st)? I don't know if it helps at all, but this issue is not happening on all of our cluster nodes. We had 4 new nodes installed in the last weeks and I think they might not have the exact same OS version. I've checked for the python version anyway, and on our previous nodes (the ones where this issue is not present), we have python 2.6.5, while on the 4 newest nodes, it is python version 2.6.6. The "markupsafe" module is nowhere to be found in the package directory of python 2.6.5, but it is indeed present in the package directory of python 2.6.6 (hence why the conflict I suppose). Thank you for your help! This is much appreciated! Jean-Francois From: Dannon Baker <dannon.baker@gmail.com> To: Jean-Francois Payotte <jean-francois.payotte@dnalandmarks.ca> Cc: Galaxy Dev <galaxy-dev@lists.bx.psu.edu> Date: 19/04/2013 06:47 PM Subject: Re: [galaxy-dev] Any hint on how to use Galaxy within virtualenv? Jean-Francois, Are you running a current revision of Galaxy? This issue should be resolved in recent galaxy releases. -Dannon On Fri, Apr 19, 2013 at 3:47 PM, Jean-Francois Payotte < jean-francois.payotte@dnalandmarks.ca> wrote: 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 ___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

Hi Dannon, We did update our galaxy development instance to the latest distribution (April 1st). Unfortunately, because of some LDAP issue (we are testing to implement LDAP authentication at the same time) I didn't had time yet, to test if this would solve the "markupsafe" issue. As soon as I can find a couple minutes to test it, I will let you know the results. Thank you for your follow-up. :) Jean-Francois From: Dannon Baker <dannon.baker@gmail.com> To: Jean-Francois Payotte <jean-francois.payotte@dnalandmarks.ca> Cc: Galaxy Dev <galaxy-dev@lists.bx.psu.edu> Date: 29/04/2013 09:24 AM Subject: Re: [galaxy-dev] Any hint on how to use Galaxy within virtualenv? Hi Jean-Francois, Were you able to update to the next galaxy-dist and test? This issue should be resolved in 8771:ae446180fd11, which was added just after the distribution you were using previously. -Dannon