Hello Clare,

On Oct 16, 2012, at 1:02 AM, Clare Sloggett wrote:

> Hi all,
> I managed to break a toolshed-installed tool by fiddling with the
> files under shed_tools.

As you've discovered, this is not a good thing to try.  Always use the Galaxy 
interface features to perform tasks like this.

> 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,
> either.

Depending on the changes you've made, you should be able to do the following:

1. Manually remove the installed repository subdirectory hierarchy from disk.
2. If the repository included any tools, manually remove entries for each of 
them from the shed_tool-conf.xml file ( or the equivalent file you have 
configured for handling installed repositories )
3. Manually update the database using the following command (assuming your 
installed repository is named 'bcftools_view' and it is the only repository you 
have installed with that name) - letter capitalization is required:

The following assumes you're using postgres:

update tool_shed_repository set deleted=True, uninstalled=True, 
status='Uninstalled', error_message=Null  where name = 'bcftools_view';

> 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
> currently:
> 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:
> URL: 
> http://galaxy-tut.genome.edu.au/admin_toolshed/deactivate_or_uninstall_repository?id=a25e134c184d6e4b
> 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
> deactivate_or_uninstall_repository
>>> 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
> generate_tool_panel_dict_from_shed_tool_conf_entries
>>> 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
> Thanks,
> Clare
> -- 
> 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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