Hi Greg,

Thanks for this!

On 17 October 2012 01:17, Greg Von Kuster <g...@bx.psu.edu> wrote:

>> 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.

Actually, the reason I did this was because I didn't know how to solve
a different problem, so maybe I should ask you about that one as well.

We had some occasions where we'd try to install a tool from the
toolshed, and it would hang - it appeared that the hg pull was timing
out. In these cases the config files wouldn't get set up, but a
partial repository was pulled / directories were created, and the
repository files would then get in the way of trying to install the
tool (it seemed to think it was already there). The only way to fix it
seemed to be to manually delete the partially-pulled repository under
shed_tools. This worked fine for fixing failed installs. But, this
time, I thought (wrongly) that this had happened again and I deleted a
repository - then realised that it was actually installed and
registered in the database, etc.

So, if the hg pull times out, is there a right way to clean up the
resulting files? I got in the habit of doing it manually, which of
course is dangerous, because I didn't know any way to do it via the
admin interface.

> 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';

Thanks very much! Yes it's postgres. I'll let you know if I succeed.



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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