Hi all,

I managed to break a toolshed-installed tool by fiddling with the
files under shed_tools. This led to a situation in which the Galaxy
admin interface claims the tool is still installed, but can't find any
files for it. I manually put the repository files where I think they
should go, but this didn't fix the situation, so what I really want to
do is just get rid of it altogether and reinstall cleanly. I'm not
certain that the tool was working properly before I fiddled with it,

Galaxy won't let me uninstall, deactivate or update it (because it
can't find it properly) and it won't let me install it (because it
thinks it's installed). It also seems (judging by the last of the
errors below) to be unable to find some config information that it
expects, but I don't really understand what's going on there.

So my question is: given a messy, screwed up install, how can I
completely remove it and start from scratch? What are the different
components and config files I need to remove it from and are they all
manually accessible?

Thanks in advance for any help!

If it's relevant to my question, here are some of the behaviours I see

The tool appears as "Installed" under Admin -> Manage installed tool
shed repositories, but doesn't show up in the tools panel.

If I try Repository Actions -> Get repository updates , I get the error:
The directory containing the installed repository named
'bcftools_view' cannot be found.

But if I try Repository Actions -> Reset repository metadata , it
apparently works, I get
Metadata has been reset on repository bcftools_view.

And, if I try to 'Deactivate or uninstall' the apparently-installed
repository, I get:

Module paste.exceptions.errormiddleware:144 in __call__
>>  app_iter = self.application(environ, sr_checker)
Module paste.debug.prints:106 in __call__
>>  environ, self.app)
Module paste.wsgilib:543 in intercept_output
>>  app_iter = application(environ, replacement_start_response)
Module paste.recursive:84 in __call__
>>  return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__
>>  body = method( trans, **kwargs )
Module galaxy.web.framework:205 in decorator
>>  return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.admin_toolshed:452 in
>>  remove_from_tool_panel( trans, tool_shed_repository, shed_tool_conf, 
>> uninstall=remove_from_disk_checked )
Module galaxy.util.shed_util:1781 in remove_from_tool_panel
>>  tool_panel_dict = generate_tool_panel_dict_from_shed_tool_conf_entries( 
>> trans, repository )
Module galaxy.util.shed_util:942 in
>>  tree = util.parse_xml( shed_tool_conf )
Module galaxy.util:135 in parse_xml
>>  tree = ElementTree.parse(fname)
Module elementtree.ElementTree:859 in parse
Module elementtree.ElementTree:576 in parse
TypeError: coercing to Unicode: need string or buffer, NoneType found



Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University of Melbourne, Parkville Campus
187 Grattan Street, Carlton, Melbourne
Victoria 3010, Australia
Ph: 03 903 53357          M: 0414 854 759
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