Re: [galaxy-dev] Egg distribution error

2015-01-15 Thread John Chilton 
Sorry for the delayed response - I am not really an expert on Galaxy's
egg stuff - but I believe running `python scripts/fetch_eggs.py`
before starting Galaxy usually fixes these problems for reasons I
don't understand. One probably shouldn't need to manually install mock
or pycrypto though.

Sorry for the problems and thanks for using Galaxy (and upgrading)!

-John

On Thu, Jan 15, 2015 at 10:42 AM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
 Hi all

 For what it's worth, I manually installed mock (and pycrypto because
 that was the next thing it complained about) and it worked after that.

 Ulf

 On 14/01/15 14:23, Ulf Schaefer wrote:
 Hi all

 After the announcements this morning, I upgraded to the latest stable
 release as suggested (latest_2015.01.13).

 Our server is now not starting with the following error message. Any
 ideas what I might be doing wrong?

 Thanks a lot
 Ulf

 ---

 galaxy.eggs DEBUG 2015-01-14 14:10:25,272 Fetched
 http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.6.egg
 galaxy.eggs ERROR 2015-01-14 14:10:25,290 One of Galaxy's managed eggs
 depends on something which is missing, this is almost certainly a bug in
 the egg distribution.
 galaxy.eggs ERROR 2015-01-14 14:10:25,291 Dependency bioblend requires
 mock
 Traceback (most recent call last):
 File ./scripts/paster.py, line 33, in module
   serve.run()
 File /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
 line 1049, in run
   invoke(command, command_name, options, args[1:])
 File /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
 line 1055, in invoke
   exit_code = runner.run(args)
 File /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
 line 220, in run
   result = self.command()
 File /home/galaxy/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
 /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line
 350, in loadapp
   return loadobj(APP, uri, name=name, **kw)
 File
 /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line
 375, in loadobj
   return context.create()
 File
 /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line
 813, in create
   return self.object_type.invoke(self)
 File
 /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line
 249, in invoke
   return fix_call(context.object, context.global_conf,
 **context.local_conf)
 File
 /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line
 97, in fix_call
   val = callable(*args, **kw)
 File
 /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py, line
 54, in app_factory
   webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
 File /home/galaxy/galaxy-dist/lib/galaxy/web/framework/webapp.py,
 line 119, in add_ui_controllers
   module = import_module( module_name )
 File
 /home/galaxy/galaxy-dist/lib/galaxy/util/backports/importlib/__init__.py,
 line 37, in import_module
   __import__(name)
 File
 /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py,
 line 21, in module
   eggs.require('bioblend')
 File /home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line
 411, in require
   return c[req.project_name].require()
 File /home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line
 239, in require
   dists = self.resolve()
 File /home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line
 170, in resolve
   dists = pkg_resources.working_set.resolve( (
 self.distribution.as_requirement(), ), env, self.fetch )
 File /home/galaxy/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
 (/home/galaxy/galaxy-dist/eggs/bioblend-0.4.2-py2.6.egg),
 Requirement.parse('mock'))

 ---

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Re: [galaxy-dev] Egg distribution error

2015-01-15 Thread Ulf Schaefer 
Hi all

For what it's worth, I manually installed mock (and pycrypto because 
that was the next thing it complained about) and it worked after that.

Ulf

On 14/01/15 14:23, Ulf Schaefer wrote:
 Hi all

 After the announcements this morning, I upgraded to the latest stable
 release as suggested (latest_2015.01.13).

 Our server is now not starting with the following error message. Any
 ideas what I might be doing wrong?

 Thanks a lot
 Ulf

 ---

 galaxy.eggs DEBUG 2015-01-14 14:10:25,272 Fetched
 http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.6.egg
 galaxy.eggs ERROR 2015-01-14 14:10:25,290 One of Galaxy's managed eggs
 depends on something which is missing, this is almost certainly a bug in
 the egg distribution.
 galaxy.eggs ERROR 2015-01-14 14:10:25,291 Dependency bioblend requires
 mock
 Traceback (most recent call last):
 File ./scripts/paster.py, line 33, in module
   serve.run()
 File /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
 line 1049, in run
   invoke(command, command_name, options, args[1:])
 File /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
 line 1055, in invoke
   exit_code = runner.run(args)
 File /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
 line 220, in run
   result = self.command()
 File /home/galaxy/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
 /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line
 350, in loadapp
   return loadobj(APP, uri, name=name, **kw)
 File
 /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line
 375, in loadobj
   return context.create()
 File
 /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line
 813, in create
   return self.object_type.invoke(self)
 File
 /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line
 249, in invoke
   return fix_call(context.object, context.global_conf,
 **context.local_conf)
 File
 /home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line
 97, in fix_call
   val = callable(*args, **kw)
 File
 /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py, line
 54, in app_factory
   webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
 File /home/galaxy/galaxy-dist/lib/galaxy/web/framework/webapp.py,
 line 119, in add_ui_controllers
   module = import_module( module_name )
 File
 /home/galaxy/galaxy-dist/lib/galaxy/util/backports/importlib/__init__.py,
 line 37, in import_module
   __import__(name)
 File
 /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py,
 line 21, in module
   eggs.require('bioblend')
 File /home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line
 411, in require
   return c[req.project_name].require()
 File /home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line
 239, in require
   dists = self.resolve()
 File /home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line
 170, in resolve
   dists = pkg_resources.working_set.resolve( (
 self.distribution.as_requirement(), ), env, self.fetch )
 File /home/galaxy/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
 (/home/galaxy/galaxy-dist/eggs/bioblend-0.4.2-py2.6.egg),
 Requirement.parse('mock'))

 ---

 **
 The information contained in the EMail and any attachments is confidential 
 and intended solely and for the attention and use of the named addressee(s). 
 It may not be disclosed to any other person without the express authority of 
 Public Health England, or the intended recipient, or both. If you are not the 
 intended recipient, you must not disclose, copy, distribute or retain this 
 message or any part of it. This footnote also confirms that this EMail has 
 been swept for computer viruses by Symantec.Cloud, but please re-sweep any 
 attachments before opening or saving. http://www.gov.uk/PHE
 **
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not be disclosed to any other person without the express