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
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
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.
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.
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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Please keep all replies on the list by using "reply all"
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