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_repos... 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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: