Eleanor, Can you please clarify if starting galaxy worked when you did:
. ./galaxy_env/bin/activate cd galaxy_dist sh run.sh If it didn't, activate the python environment and run: pip-2.6 install pycrypto - or - pip install pycrypto If I recall correctly, the init script shipped with Galaxy does not activate the python environment. I modified the init script to issue a login sudo in order to source the environment. In .bashrc, I have it source the python environment. This ensures that the python environment is always activated before galaxy is started regardless of how I start it. Iyad Kandalaft Bioinformatics Programmer Microbial Biodiversity Bioinformatics Science & Technology Branch Agriculture & Agri-Food Canada iyad.kandal...@agr.gc.ca | (613) 759-1228 ________________________________ From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Eleanor Morgan [e.mor...@curtin.edu.au] Sent: July 16, 2014 10:35 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Unable to update to latest version of galaxy Hi all, I am new to galaxy. We have a local install that we intend to turn into a production server at some stage. We initially installed galaxy using the April 2014 version. We set up a Virtual Python Environment following the instructions set out on this page: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use_a_clean_environment When I updated to the June version of galaxy and tried to start up the server using the recommended shell script placed in /etc/init.d I got the following error message: Starting galaxy... Some eggs are out of date, attempting to fetch... Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 37, in <module> c.resolve() # Only fetch eggs required by the config File "/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/usr/lib/python2.6/site-packages/pkg_resources.py", line 550, in resolve raise VersionConflict(dist,req) # XXX put more info here pkg_resources.VersionConflict: (pycrypto 2.0.1 (/usr/lib64/python2.6/site-packages), Requirement.parse('pycrypto>=2.1,!=2.4')) Fetch failed. …done. This error message implies that I need to update pycrypto on our system, but my understanding is that the virtual python environment takes care of these sorts of dependencies. Can someone please advise? Here are two series of commands that I tried to start the system: First attempt: sudo bash /etc/init.d/galaxy stop su - galaxy cd /galaxy/galaxy-dist hg pull hg update latest_2014.06.02 exit /etc/init.d/galaxy start After galaxy start failed I tried: su – galaxy cd /galaxy . ./galaxy_env/bin/activate cd galaxy_dist sh run.sh I also tried reinstalling the virtual environment to no avail. Regards, Eleanor ___________________________________________________________ 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/
