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
>
>
___________________________________________________________
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:
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