Hello Louise,

Can you send me your community_wsgi.ini file?  I assume your copied it from 
community_wsgi.ini.sample, but somehow it looks like your configuration 
settings are attempting to start the Galaxy server instead of the tool shed 
server.  I should be able to sort it out for you by looking at your 
configuration file.

Thanks,

Greg Von Kuster

On Nov 24, 2011, at 10:34 AM, Louise-Amélie Schmitt wrote:

> Hello Greg
> 
> We tried to run the toolshed like you explained (thanks a lot for the quick 
> answer btw), it starts fine, but when we try to access it on the web, we get 
> this error in the browser:
> 
> Server Error
> An error occurred. See the error logs for more information. (Turn debug on to 
> display exception reports here)
> 
> In the logs, here is what we get:
> 
> Error - <type 'exceptions.AttributeError'>: 'Configuration' object has no 
> attribute 'ucsc_display_sites'
> URL: http://taiji/
> File 
> '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
>  line 143 in __call__
> app_iter = self.application(environ, start_response)
> File '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', 
> line 80 in __call__
> return self.application(environ, start_response)
> File 
> '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', 
> line 632 in __call__
> return self.application(environ, start_response)
> File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/base.py', line 134 in 
> __call__
> trans = self.transaction_factory( environ )
> File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 187 
> in <lambda>
> self.set_transaction_factory( lambda e: self.transaction_chooser( e, 
> galaxy_app, session_cookie ) )
> File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 207 
> in transaction_chooser
> return GalaxyWebUITransaction( environ, galaxy_app, self, session_cookie )
> File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 860 
> in __init__
> self._ensure_logged_in_user( environ )
> File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 420 
> in _ensure_logged_in_user
> if self.app.config.ucsc_display_sites and self.request.path == display_as:
> AttributeError: 'Configuration' object has no attribute 'ucsc_display_sites'
> 
> Since this name ringed a bell, I checked the universe_wsgi.ini and found this 
> "Display sites" section. I therefore copied it and pasted it in the 
> community.wsgi.ini file and uncommented the variables in this section. But 
> when we tried again, we still get the same error.
> 
> What is confusing, is that after the error message, all the CGI, 
> congifuration and WSGI variables are displayed, and in the configuration 
> section we have this line:
> ucsc_display_sites: 'main,test,archaea,ucla'
> 
> Did we miss anything? Where should we start searching for a possible error 
> source?
> 
> Thanks,
> L-A
> 
> 
> 
> Le 23/11/2011 16:11, Greg Von Kuster a écrit :
>> Hello Nicolas,
>> 
>> On Nov 22, 2011, at 11:04 AM, Nicolas Delhomme wrote:
>> 
>>> Hi Greg,
>>> 
>>> I've been scanning the mailing list, but wasn't lucky enough to find the 
>>> answer I was looking for.
>>> 
>>> Basically, we would be interested to have our own Galaxy Tool Shed 
>>> in-house, to develop and test tools within our local Galaxy instance. What 
>>> I'm thinking of, is to use the power of the tool shed to develop new 
>>> algorithm, new tools, etc. that could be published afterwards.
>> 
>> This is great, but keep in mind that the intent of the tool shed (whether it 
>> is a local, proprietary tool shed or the public Galaxy tool shed) is to 
>> provide a vehicle for sharing tools (and tool-related objects like 
>> workflows, data types, etc) that are determined to be functional within a 
>> Galaxy instance.  So the primary use of a tool shed should be to enable 
>> sharing.  The tools themselves should be implemented within a development 
>> environment that includes a Galaxy instance, and when a tool is deemed 
>> functional, it can then be uploaded to the tool shed for sharing.
>> 
>> You can, however, tweak the primary intent of a tool shed to meet your 
>> needs.  In your case, it seems that you may be interested in using a local 
>> tool shed instance to share tools between developers during the development 
>> process.  If this is the case, then your approach can be one where a 
>> developer creates a repository on the local tool shed multiple developers 
>> can clone it.  The mercurial command line process for committing, pushing, 
>> pulling and updating can be used to share updates to the tool code by 
>> multiple developers throughout the process.
>> 
>> If a single developer is implementing the tool however, it may make more 
>> sense to not use the tool shed as part of the development process - just 
>> upload the tool when it is functional.
>> 
>> 
>>> Because these would be sensitive material, we would not want to put them 
>>> right away on the public test Tool Shed. Having a local Tool Shed instance 
>>> would still be very helpful in releasing these tools to the community 
>>> afterwards, as they would have been integrated and developed within that 
>>> framework from the start.
>> This is a good approach.
>> 
>>> Any pointers on how to achieve this are welcome as I'm not so familiar with 
>>> the Tool Shed yet, e.g. would making a local clone of the tool shed 
>>> repository be enough?
>> Make sure to read the tool shed wiki at 
>> http://wiki.g2.bx.psu.edu/Tool%20Shed.  I make sure to keep this up-to-date 
>> with the latest features of the tool shed.  You'll ffind, however, that 
>> there are some tool shed admin user features that have not yet been 
>> documented.  If you have any question, let me know.
>> 
>> The tool shed is included in the Galaxy distribution, so no additional 
>> cloning is necessary - it is just a different webpp from Galaxy itself.  It 
>> uses a different database from Galaxy, which you configure in the file 
>> community_wsgi.ini (the equivalent of universe_wsgi.ini for Galxy).  After 
>> you have the configuration settings as you want them, start up your local 
>> tool shed by:
>> 
>> %sh run_community.sh
>> 
>> Feel free to ask questions!
>> 
>> 
>>> Thanks,
>>> 
>>> Nico
>>> 
>>> 
>>> ---------------------------------------------------------------
>>> Nicolas Delhomme
>>> 
>>> Genome Biology Computational Support
>>> 
>>> European Molecular Biology Laboratory
>>> 
>>> Tel: +49 6221 387 8310
>>> Email: nicolas.delho...@embl.de
>>> Meyerhofstrasse 1 - Postfach 10.2209
>>> 69102 Heidelberg, Germany
>>> ---------------------------------------------------------------
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> ___________________________________________________________
>>> 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/
>> Greg Von Kuster
>> Galaxy Development Team
>> g...@bx.psu.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/
> 
> ___________________________________________________________
> 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/
> 

Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu




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