Hi Hans, Thank you for your advice. Thanks to other advice received from Iyad, I was able to work out that my virtual python environment wasn¹t functioning correctly. After I reinstalled it I managed to get going on the update. However, I will keep this email on hand for future updates!
Regards, Eleanor On 17/07/2014 3:26 pm, "Hans-Rudolf Hotz" <h...@fmi.ch> wrote: >Hi Eleanor > > >I was running into the same problem when I did the updates for our >servers (from release_2013.11.04 to release_2014.04.14), eg: > >... >pkg_resources.VersionConflict: (pycrypto 2.0.1 >(/usr/lib64/python2.6/site-packages), >Requirement.parse('pycrypto>=2.1,!=2.4')) >Fetch failed. > > >I solved it by deleting the contents of ~/galaxy_dist/eggs/ and fetched >all eggs again (not just the new/updated ones). This somehow solved the >problem, by using the (re-fetched) 'pycrypto' from ~/galaxy_dist/eggs/ >instead of the one provided by the system. > > > >Regards, Hans-Rudolf > > > > > > > >On 07/17/2014 04:35 AM, Eleanor Morgan wrote: >> 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 Some eggs are out of date, attempting to fetch...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, e.args ) >> >> 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. >> >> Šdone. >> >> >> 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/ >> ___________________________________________________________ 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/