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 feature.
Greg Von Kuster
On Sep 11, 2012, at 11:48 PM, Oleksandr Moskalenko wrote:
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  on any action afterwards?
1. "Server Error. An error occurred. See the error logs for more information. (Turn
debug on to display exception reports here)"