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...)
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 djm29@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 Some eggs are out of date, attempting to fetch...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
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