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Some eggs are out of date, attempting to fetch...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