Egg distribution error

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Ulf
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Egg distribution error

Ulf
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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Ulf
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Re: Egg distribution error

Ulf
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
> **************************************************************************
> ___________________________________________________________
> 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:
>    https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/
>

**************************************************************************
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
**************************************************************************
___________________________________________________________
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:
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Re: Egg distribution error

John Chilton-4
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 <[hidden email]> 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'))
>>
>> ---
>>
>> **************************************************************************
>> 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
>> **************************************************************************
>> ___________________________________________________________
>> 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:
>>    https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>    http://galaxyproject.org/search/mailinglists/
>>
>
> **************************************************************************
> 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
> **************************************************************************
> ___________________________________________________________
> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/