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:


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Some eggs are out of date, attempting to fetch...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


  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 

    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.


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
/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.


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