Hello Clare,

On Oct 17, 2012, at 2:22 AM, Clare Sloggett wrote:

> 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.


Was the timeout a regular occurrence?  if so, do you know that cause, and were 
you able to get it resolved?


> 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.

The October 5, 2012 Galaxy distribution news brief includes the following link 
to information about the process for handling repository installation errors, 
specifically when the errors occur during cloning.

http://wiki.g2.bx.psu.edu/InstallingRepositoriesToGalaxy#Handling_repository_installation_errors

If you're running an older version of Galaxy, you'll need to update to the 
October 5 release in order to have these features.

The news brief release information is:

upgrade: $ hg pull -u -r b5bda7a5c345
Let me know if this is not what you're looking for.

Thanks,

Greg Von Kuster


> 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.
> 
> 
> 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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