Hi Matthias,

You uncovered an issue I recently introduced and which I've fixed in change set 
7277:4a1389e037c6, which is now running on both public Galaxy tool sheds.  
Sorry for the back and forth on this - your line numbers in your paster log 
threw me since they were significantly different from mine.

Thanks for reporting this problem!

Greg Von Kuster

> On 06/15/2012 02:58 PM, Greg Von Kuster wrote:
>> 
>> Hi Matthias,
>> 
>> There is really nothing to configure in your Galaxy environment in order to 
>> use the public Galaxy tool sheds.  Ideally, you should set the following 
>> configuration setting, but not setting it defaults to using the file named 
>> shed_tool_conf.xml for installed tools anyway.
>> 
>> tool_config_files = tool_conf.xml,shed_tool_conf.xml
>> 
>> The current Galaxy central repository tip is 7276:622fd4f0a437, which you 
>> should pull.  This is the revision that the public tool sheds are using - 
>> they generally always run the Galaxy central tip revision.
>> 
>> It's very possible that since you updated after 6 months of development, 
>> your repository has some issues.  What are the results of the following 
>> commands?
>> 
>> hg diff
>> 
>> hg status
>> 
>> hg verify
>> 
>> hg summary
>> 
>> 
>> 
>> On Jun 15, 2012, at 7:55 AM, Hollander, Mattias de wrote:
>> 
>>> Hi Greg,
>>> 
>>> I guess something went wrong while update, because I updated to the 
>>> latest changeset:
>>> 
>>> hg tip | grep changeset
>>> changeset:   7262:4fbd05095ca7
>>> 
>>> Can it be because I the last time I updated was at least half a year ago 
>>> and the toolshed integration has been implemented afterwards? So that I 
>>> need to configure the toolshed before I can install something form the 
>>> public one?
>>> 
>>> Thanks!
>>> 
>>> Mattias
>>> 
>>> 
>>> On 06/13/2012 05:43 PM, Greg Von Kuster wrote:
>>>> Hello Mattias,
>>>> 
>>>> Did you pull from the Galaxy central repo?  The latest change set is 
>>>> 7262:4fbd05095ca7, which is what you should be running in order to use the 
>>>> tool shed.  Let me know if you in fact have the latest from central - your 
>>>> line numbers in your log below look to be different from mine.
>>>> 
>>>> Thanks,
>>>> 
>>>> Greg Von Kuster
>>>> 
>>>> On Jun 13, 2012, at 11:38 AM, Hollander, Mattias de wrote:
>>>> 
>>>>> Hi,
>>>>> 
>>>>> I just updated my local Galaxy installation to the latest version. I am
>>>>> trying out the feature to add tools directly from the toolshed, but this
>>>>> is not working. It results in this error:
>>>>> 
>>>>> File 
>>>>> '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/exceptions/errormiddleware.py',
>>>>>  line 144 in __call__
>>>>>   app_iter = self.application(environ, sr_checker)
>>>>> File 
>>>>> '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py',
>>>>>  line 106 in __call__
>>>>>   environ, self.app)
>>>>> File 
>>>>> '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py',
>>>>>  line 543 in intercept_output
>>>>>   app_iter = application(environ, replacement_start_response)
>>>>> File 
>>>>> '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
>>>>>  line 84 in __call__
>>>>>   return self.application(environ, start_response)
>>>>> File 
>>>>> '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
>>>>>  line 633 in __call__
>>>>>   return self.application(environ, start_response)
>>>>> File '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/base.py', 
>>>>> line 160 in __call__
>>>>>   body = method( trans, **kwargs )
>>>>> File 
>>>>> '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/__init__.py', 
>>>>> line 184 in decorator
>>>>>   return func( self, trans, *args, **kwargs )
>>>>> File 
>>>>> '/home/galaxyTools/galaxy-central/lib/galaxy/web/controllers/admin_toolshed.py',
>>>>>  line 481 in install_repository
>>>>>   install_tool_dependencies=install_tool_dependencies )
>>>>> File '/home/galaxyTools/galaxy-central/lib/galaxy/util/shed_util.py', 
>>>>> line 1228 in load_repository_contents
>>>>>   dist_to_shed=False )
>>>>> File '/home/galaxyTools/galaxy-central/lib/galaxy/util/shed_util.py', 
>>>>> line 342 in create_or_update_tool_shed_repository
>>>>>   installed_changeset_revision=changeset_revision,
>>>>> NameError: global name 'changeset_revision' is not defined
>>>>> 
>>>>> 
>>>>> 
>>>>> And my shed_tools_conf.xml looks like this:
>>>>> 
>>>>> <?xml version="1.0"?>
>>>>> <toolbox tool_path="../shed_tools">
>>>>> </toolbox>
>>>>> 
>>>>> 
>>>>> Should I put more configuration in this file?
>>>>> 
>>>>> Any help is appreciated.
>>>>> 
>>>>> Thanks!
>>>>> 
>>>>> Mattias
>>>>> ___________________________________________________________
>>>>> Please keep all replies on the list by using "reply all"
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>>>>> and other Galaxy lists, please use the interface at:
>>>>> 
>>>>>  http://lists.bx.psu.edu/
>>> 
>> 
> 

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