So the problem now is that you have conflicting eggs on your system path
that are getting loaded prior to the galaxy supplied eggs.  Galaxy manages
its own dependencies, and not relying on those installed via pip/etc.

The simplest, most fool-proof solution here is to use a virtualenv and
start galaxy in a clean environment.  See the virtualenv bit here:
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer

Basically, you're going to want to:

pip install virtualenv
virtualenv env_galaxy_clean
source env_galaxy_clean/bin/activate
sh run.sh (or otherwise launch galaxy from within this new environment)


On Wed, Jun 4, 2014 at 10:25 AM, Nikos Sidiropoulos <nikos.sid...@gmail.com>
wrote:

>
> Dannon,
>
> `python scripts/fetch_eggs.py` failed with errors about more packages
> (pycrypto, poster).
>
> After installing them and running the 'fetch_eggs' script successfully I'm
> getting this error upon starting the server:
>
> galaxy.eggs ERROR 2014-06-04 16:20:40,694 Dependency "bioblend" requires
> "simplejson"
>
> Traceback (most recent call last):
>   File "./scripts/paster.py", line 33, in <module>
>     serve.run()
>   File
> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py",
> line 1049, in run
>     invoke(command, command_name, options, args[1:])
>   File
> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py",
> line 1055, in invoke
>
>     exit_code = runner.run(args)
>   File
> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py",
> line 220, in run
>     result = self.command()
>   File
> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py",
> line 643, in command
>     app = loadapp( app_spec, name=app_name, relative_to=base,
> global_conf=vars)
>   File
> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
> line 350, in loadapp
>     return loadobj(APP, uri, name=name, **kw)
>   File
> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
> line 375, in loadobj
>     return context.create()
>   File
> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
> line 813, in create
>     return self.object_type.invoke(self)
>   File
> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
> line 249, in invoke
>     return fix_call(context.object, context.global_conf,
> **context.local_conf)
>   File
> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
> line 97, in fix_call
>     val = callable(*args, **kw)
>   File
> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py",
> line 49, in app_factory
>     webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
>   File
> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/web/framework/__init__.py",
> line 441, in add_ui_controllers
>     module = import_module( module_name )
>   File
> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/backports/importlib/__init__.py",
> line 37, in import_module
>     __import__(name)
>   File
> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py",
> line 20, in <module>
>     eggs.require('bioblend')
>   File
> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py",
> line 409, in require
>     return c[req.project_name].require()
>   File
> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py",
> line 237, in require
>     dists = self.resolve()
>   File
> "/steno-internal/projects/galaxy-test/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
> "/steno-internal/projects/galaxy-test/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
> (/steno-internal/projects/galaxy-test/galaxy-dist/eggs/bioblend-0.4.2-py2.7.egg),
> Requirement.parse('simplejson'))
>
> Simplejson is installed in the system and the library folder is in the
> galaxy user's PYTHONPATH.
>
>
> On 4 June 2014 15:32, Evan Bollig <boll0...@umn.edu> wrote:
>
>> Dannon,
>>
>> Do you guys have a web page that documents all of the script/ utilities?
>> I know most of my deployment and upgrade problems have been resolved by
>> various scripts in there, but I have no idea what's available until I turn
>> to this mailing list.
>>
>> -E
>>
>>
>> On Wednesday, June 4, 2014, Dannon Baker <dannon.ba...@gmail.com> wrote:
>>
>>> Hey Nikos,
>>>
>>> I think you're seeing the same issue from this trello card here:
>>> https://trello.com/c/HWuxsftB/1596-fetching-zip-safe-eggs-that-depend-on-other-eggs-will-fail
>>>
>>> Can you run `python scripts/fetch_eggs.py` from your galaxy directory?
>>>  That should re-fetch galaxy's eggs and you should be up and running again.
>>>
>>>
>>> On Wed, Jun 4, 2014 at 9:15 AM, Nikos Sidiropoulos <
>>> nikos.sid...@gmail.com> wrote:
>>>
>>>> Hi all,
>>>>
>>>> after the latest galaxy update I've experienced the following error
>>>> while trying to start the server.
>>>>
>>>> galaxy.eggs DEBUG 2014-06-04 14:34:56,027 Fetched
>>>> http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg
>>>> galaxy.eggs ERROR 2014-06-04 14:34:56,047 One of Galaxy's managed eggs
>>>> depends on something which is missing, this is almost certainly a bug in t
>>>> he egg distribution.
>>>> galaxy.eggs ERROR 2014-06-04 14:34:56,047 Dependency "bioblend"
>>>> requires "mock"
>>>> Traceback (most recent call last):
>>>>   File "./scripts/paster.py", line 33, in <module>
>>>>     serve.run()
>>>>   File
>>>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py",
>>>> line 1049, in run
>>>>     invoke(command, command_name, options, args[1:])
>>>>   File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util
>>>> /pastescript/serve.py", line 1055, in invoke
>>>>     exit_code = runner.run(args)
>>>>   File
>>>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py",
>>>> line 220, in run
>>>>     result = self.command()
>>>>   File
>>>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py",
>>>> line 643, in command
>>>>     app = loadapp( app_spec, name=app_name, relative_to=base,
>>>> global_conf=vars)
>>>>   File
>>>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
>>>> line 350, in loadapp
>>>>     return loadobj(APP, uri, name=name, **kw)
>>>>   File
>>>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
>>>> line 375, in loadobj
>>>>     return context.create()
>>>>   File
>>>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
>>>> line 813, in create
>>>>     return self.object_type.invoke(self)
>>>>   File
>>>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
>>>> line 249, in invoke
>>>>     return fix_call(context.object, context.global_conf,
>>>> **context.local_conf)
>>>>   File
>>>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
>>>> line 97, in fix_call
>>>>     val = callable(*args, **kw)
>>>>   File
>>>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py",
>>>> line 49, in app_factory
>>>>     webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app
>>>> )
>>>>   File
>>>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/web/framework/__init__.py",
>>>> line 441, in add_ui_controllers
>>>>     module = import_module( module_name )
>>>>   File
>>>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/backports/importlib/__init__.py",
>>>> line 37, in import_module
>>>>     __import__(name)
>>>>   File
>>>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py",
>>>> line 20, in <module>
>>>>     eggs.require('bioblend')
>>>>   File
>>>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py",
>>>> line 409, in require
>>>>     return c[req.project_name].require()
>>>>   File
>>>> "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py",
>>>> line 237, in require
>>>>     dists = self.resolve()
>>>>   File
>>>> "/steno-internal/projects/galaxy-test/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
>>>> "/steno-internal/projects/galaxy-test/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
>>>> (/steno-internal/projects/galaxy-test/galaxy-dist/eggs/bioblend-0.4.2-py2.7.egg),
>>>> Requirement.parse('mock'))
>>>>
>>>>
>>>> First I got and error about the python module 'requests' missing, fixed
>>>> it using 'pip install', and then got the error above.
>>>>
>>>> Regards,
>>>> Nikos
>>>>
>>>> ___________________________________________________________
>>>> Please keep all replies on the list by using "reply all"
>>>> in your mail client.  To manage your subscriptions to this
>>>> and other Galaxy lists, please use the interface at:
>>>>   http://lists.bx.psu.edu/
>>>>
>>>> To search Galaxy mailing lists use the unified search at:
>>>>   http://galaxyproject.org/search/mailinglists/
>>>>
>>>
>>>
>>
>> --
>> -Evan Bollig
>> Research Associate | Application Developer | User Support Consultant
>> Minnesota Supercomputing Institute
>> 599 Walter Library
>> 612 624 1447
>> e...@msi.umn.edu
>> boll0...@umn.edu
>>
>>
>
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