Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents

2013-10-24 Thread Peter Cock
On Thu, Oct 24, 2013 at 12:09 PM, Lukasse, Pieter pieter.luka...@wur.nl wrote: Hi , I have a toolshed repository where I expect 5 tools to appear in the “Contents of this repository” section but one of them fails to appear in the list (see screenshot). Where can I find out what is going

Re: [galaxy-dev] Tool Shed Tests failing with sniffer/ftype problem

2013-10-24 Thread Peter Cock
On Fri, Oct 11, 2013 at 10:01 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Aug 1, 2013 at 8:43 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, As of 10290:d34d6d1da813, nsltradamus and effectivet3 should start returning valid test results. As for seq_rename, ... --Dave B. Hi

Re: [galaxy-dev] Toolshed reset all repository metadata

2013-10-24 Thread Greg Von Kuster
Hello Simon, On Oct 23, 2013, at 5:01 PM, Simon Guest simon.gu...@agresearch.co.nz wrote: We've noticed a funny about resetting repository metadata from the toolshed web interface. My understanding is that this is used to get the toolshed back in sync with the underlying mercurial repo,

Re: [galaxy-dev] Installing toolshed repositories with set_environment dependency

2013-10-24 Thread Greg Von Kuster
Hello Saskia, This was indeed a bug (not abut which was a spell checker spelling error) which has been resolved in 6:83bed9c7dbbc. This fix has been committed to the next-stable branch and is currently running on both the test and main Galaxy tool sheds. Thanks for reporting this issue.

Re: [galaxy-dev] Defining $GALAXY_SLOTS for use in tool wrappers

2013-10-24 Thread Peter Cock
On Thu, Oct 17, 2013 at 8:37 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Am Samstag, den 12.10.2013, 19:42 +0100 schrieb Peter Cock: On Thu, Aug 1, 2013 at 10:27 AM, Nicola Soranzo sora...@crs4.it wrote: Il 2013-07-30 17:18 Peter Cock ha scritto: Hello all, Re:

Re: [galaxy-dev] Defining $GALAXY_SLOTS for use in tool wrappers

2013-10-24 Thread James Taylor
So far $GALAXY_SLOTS seems to be working nicely for me. However, I am wondering if it would be possible to use it inside the configfile section? Is that run at the time of job creation on the Galaxy server (where determining the number of threads may be hard) or as part of job execution

Re: [galaxy-dev] Defining $GALAXY_SLOTS for use in tool wrappers

2013-10-24 Thread Peter Cock
On Thu, Oct 24, 2013 at 5:53 PM, James Taylor ja...@jamestaylor.org wrote: So far $GALAXY_SLOTS seems to be working nicely for me. However, I am wondering if it would be possible to use it inside the configfile section? Is that run at the time of job creation on the Galaxy server (where

Re: [galaxy-dev] Toolshed reset all repository metadata

2013-10-24 Thread Guest, Simon
At Thu, 24 Oct 2013 10:03:14 -0400, Greg Von Kuster wrote: Hello Simon, On Oct 23, 2013, at 5:01 PM, Simon Guest simon.gu...@agresearch.co.nz wrote: We've noticed a funny about resetting repository metadata from the toolshed web interface. My understanding is that this is used to

Re: [galaxy-dev] Toolshed reset all repository metadata

2013-10-24 Thread Greg Von Kuster
Hello Simon, On Oct 24, 2013, at 4:06 PM, Guest, Simon simon.gu...@agresearch.co.nz wrote: Hi Greg, Thanks for the explanation, and the link to that helpful Wiki page. And also that code update 4:71c35dbde130 which will help our tool test/development cycle. I have a remaining