Hey Peter, When you are deleting and reinstalling the tool - can you confirm for me that you are definitely deleting the tool and not just deactivating it? I don't know where to hack around from there - I think repositories are tracked in the database (tool_shed_repository) table, in shed_tool_conf.xml, integrated_tool_panel.xml, shed_tools directory, tool_dependencies directory. It would be interesting to know which of these still have references to the tool after you delete it. I am also interested in the underlying bug - are you running multiple Galaxy processes? Can you send me the tool that produced this error? -John On Tue, Aug 12, 2014 at 10:08 AM, Peter van Heusden <pvh@sanbi.ac.za> wrote:
Hi there
I updated a tool of mine recently, committed to the local toolshed, did the update from within the Admin panel and then got this error:
Error - <type 'exceptions.AttributeError'>: 'Tool' object has no attribute 'citations'
A restart of Galaxy seemed to fix the problem, but since then the tool could not be found - it is not in any of the Tool categories. Deleting and re-installing the tool does not fix this problem - and on installation time I never get asked what group to add it to. It seems as if it is somehow "stuck" in an incorrect state.
Any ideas where to go poking? Presumably there is somewhere in the database to go poking to "reset" things.
Thanks, Peter P.S. this is with the latest Galaxy from galaxy-central.
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