To get the repositories out of the limbo state, you'll have to get into your 
database and run the following sql command.  Doing this will allow you to 
install those repositories that were in limbo.  After they are installed, you 
can uninstall them if you want to.  The case on the Strings is necessary.

update tool_shed_repository set status = 'New' where status = 'Cloning';

It was great to talk with you at the conference as well!

Greg

On Aug 3, 2012, at 8:36 PM, Nikhil Joshi wrote:

> Hi Greg,
> 
> So I looked at the the URL from the log file and it was trying to
> write to a tmp directory owned by root, so that was a problem.  I
> traced the problem to a python function (make_tmp_directory) where it
> was using the environment variable "TMPDIR", which was not defined.
> So in our launch script we defined the variable and that seemed to
> work.  However, the repositories that I installed before fixing this
> are in a limbo state.  When I try to uninstall them I get that same
> AttributeError below.  Any ideas on how I can reset my installed
> Galaxy toolshed repositories so that they are not in a limbo state?
> I've included the entire traceback below:
> 
> Error Traceback:
> View as:   Interactive  |  Text  |  XML (full)
> ⇝ AttributeError: 'NoneType' object has no attribute 'startswith'
> URL: 
> http://optidavis.genomecenter.ucdavis.edu:8080/admin_toolshed/browse_repositories?operation=deactivate+or+uninstall&id=33b43b4e7093c91f
> Module weberror.evalexception.middleware:364 in respond         view
>>> app_iter = self.application(environ, detect_start_response)
> Module paste.debug.prints:98 in __call__         view
>>> environ, self.app)
> Module paste.wsgilib:539 in intercept_output         view
>>> app_iter = application(environ, replacement_start_response)
> Module paste.recursive:80 in __call__         view
>>> return self.application(environ, start_response)
> Module paste.httpexceptions:632 in __call__         view
>>> return self.application(environ, start_response)
> Module galaxy.web.framework.base:160 in __call__         view
>>> body = method( trans, **kwargs )
> Module galaxy.web.framework:184 in decorator         view
>>> return func( self, trans, *args, **kwargs )
> Module galaxy.web.controllers.admin_toolshed:356 in
> browse_repositories         view
>>> return self.deactivate_or_uninstall_repository( trans, **kwd )
> Module galaxy.web.framework:184 in decorator         view
>>> return func( self, trans, *args, **kwargs )
> Module galaxy.web.controllers.admin_toolshed:408 in
> deactivate_or_uninstall_repository         view
>>> repository_install_dir = os.path.abspath ( relative_install_dir )
> Module posixpath:343 in abspath         view
>>> if not isabs(path):
> Module posixpath:53 in isabs         view
>>> return s.startswith('/')
> AttributeError: 'NoneType' object has no attribute 'startswith'
> 
> Any help is highly appreciated!  BTW, it was really nice to get to
> talk to you at the conference. :)
> 
> - Nik.
> 
> 
> On Fri, Aug 3, 2012 at 3:49 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>> Hello Nikhil,
>> 
>> 
>> On Aug 2, 2012, at 9:32 PM, Nikhil Joshi wrote:
>> 
>>> Hi all,
>>> 
>>> We just upgraded our local galaxy to the latest version and now I am
>>> trying to get automatic tool installation to work properly.  I changed
>>> the universe_wsgi.ini file to enable the toolshed xml file,
>> 
>> Regarding this, do you mean that you have something like the following 
>> setting?
>> 
>> tool_config_files = tool_conf.xml,shed_tool_conf.xml
>> 
>> 
>>> I created
>>> a "shed_tools" directory one above the galaxy install, and restarted
>>> galaxy.  But when I try to install a repository, I get this error as a
>>> popup: "Initializing repository installation failed".
>> 
>> From what tool shed are you trying to install Galaxy?  When this pop-up is 
>> displayed, the last line of your Galaxy paster log should be a url.  If you 
>> paste that url into a browser it will display a page that displays the 
>> entire stack trace for the exception.  We'll need to see this information in 
>> order to determine the cause of the problem.
>> 
>> 
>>> I tried this
>>> with various repositories, but I get the same error.  Then when I go
>>> to "Manage installed tool shed repositories", all of the repositories
>>> I tried to install are stuck in the "Cloning" state.  Finally, if I
>>> try to uninstall any of them, I get this error, with a traceback:
>>> 
>>> AttributeError: 'NoneType' object has no attribute 'startswith'
>>> 
>>> Any ideas?
>>> 
>>> - Nik.
>>> 
>>> --
>>> Nikhil Joshi
>>> Bioinformatics Analyst/Programmer
>>> UC Davis Bioinformatics Core
>>> http://bioinformatics.ucdavis.edu/
>>> najoshi -at- ucdavis -dot- edu
>>> 530.752.2698 (w)
>>> ___________________________________________________________
>>> 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/
>> 
> 
> 
> 
> -- 
> Nikhil Joshi
> Bioinformatics Analyst/Programmer
> UC Davis Bioinformatics Core
> http://bioinformatics.ucdavis.edu/
> najoshi -at- ucdavis -dot- edu
> 530.752.2698 (w)
> 


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