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
> <javascript:_e(%7B%7D,'cvml','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
>>
>> ___________________________________________________________
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>>
>
>

-- 
-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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