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" <hrh@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Some eggs are out of date, attempting to fetch...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[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.

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

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