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.baker@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-oth...
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.sidiro@gmail.com <javascript:_e(%7B%7D,'cvml','nikos.sidiro@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 evan@msi.umn.edu boll0107@umn.edu