Hi Alex,

Assuming the installed repository is stuck in a "Cloning" state (you can see 
this by clicking the Admin menu link "Manage installed tool shed 
repositories"), you can fix it by manually running the following sql command in 
your db environment (string case is required).

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

If the status is not 'Cloning', you may need to remove the directory where the 
repository was in the process of being cloned as well, and perhaps manually 
delete the any tool entries from you shed_tool_conf.xml file.

This process is currently manual, but the next release of Galaxy (coming in 
about 10 days) will provide the ability to do this via a Galaxy Admin UI 

Greg Von Kuster

On Sep 11, 2012, at 11:48 PM, Oleksandr Moskalenko wrote:

> Hi Greg,
> What's the best way to completely clean up a borked repository on disk and in 
> the Galaxy database that failed to install for any odd reason, but hangs 
> around causing Apache server errors [1] on any action afterwards?
> Thanks,
> Alex
> 1. "Server Error. An error occurred. See the error logs for more information. 
> (Turn debug on to display exception reports here)"

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