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 Some eggs are out of date, attempting to fetch...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