Thanks for the fast reply! I tried it in the clean environment and it works. I somehow totally missed that step when setting this up! So do I need to add these 2 steps to my startup script?
/usr/bin/python2.6 virtualenv.py --no-site-packages galaxy_env . ./galaxy_env/bin/activate Thanks, Dori -----Original Message----- From: Dannon Baker [mailto:dannon.ba...@gmail.com] Sent: Tuesday, July 29, 2014 10:00 AM To: Sajdak, Doris Cc: Galaxy Dev Subject: Re: [galaxy-dev] galaxy won't start Hi Dori, If you haven't updated galaxy or manipulated the eggs at all, then it might be an updated system python module interfering with galaxy's resolution of the pyyaml we ship. Can you try running galaxy from an clean virtualenv? (https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use_a_clean_environment) If that's not it, or you'd rather try something else, I'd probably suggest wiping out galaxy's eggs (or just moving the folder to eggs_backup or the like) to force Galaxy to fetch all new eggs at the next restart, and see if that resolves it. -Dannon On Jul 29, 2014, at 9:40 AM, Sajdak, Doris <dj...@buffalo.edu> wrote: > I'm suddenly getting this error today when I tried to restart Galaxy: > > Starting galaxy... > Some eggs are out of date, attempting to fetch... > Warning: setuptools (a dependent egg of sqlalchemy-migrate) cannot be > fetched Fetched > http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg > One of Galaxy's managed eggs depends on something which is missing, this is > almost certainly a bug in the egg distribution. > Dependency "bioblend" requires "pyyaml" > Traceback (most recent call last): > File "./scripts/fetch_eggs.py", line 37, in <module> > c.resolve() # Only fetch eggs required by the config > File "/ifs/user/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, > in resolve > egg.resolve() > File "/ifs/user/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 168, > in resolve > dists = pkg_resources.working_set.resolve( ( > self.distribution.as_requirement(), ), env, self.fetch ) > File "/ifs/user/galaxy/galaxy-dist/lib/pkg_resources.py", line 569, in > resolve > raise VersionConflict(dist,req) # XXX put more info here > pkg_resources.VersionConflict: (bioblend 0.4.2 > (/ifs/user/galaxy/galaxy-dist/eggs/bioblend-0.4.2-py2.7.egg), > Requirement.parse('pyyaml')) > > pyyaml is installed and I haven't updated anything that would cause a > conflict. What do I do to fix this? > > Thanks, > Dori > > ********************************** > Dori Sajdak > Senior Systems Administrator > State University of NY at Buffalo > Center for Computational Research > 701 Ellicott St > Buffalo, NY 14203 > Phone: (716) 881-8934 > Fax: (716) 849-6656 > Web: http://ccr.buffalo.edu > ********************************** > > > ___________________________________________________________ > 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/
