On Thu, Oct 17, 2013 at 8:37 AM, Bjoern Gruening <bjoern.gruening@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 <soranzo@crs4.it> wrote:
Il 2013-07-30 17:18 Peter Cock ha scritto:
Hello all,
Re: http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010153.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-October/011557.html
Something I raised during the GCC2013, and we talked about via Twitter as well was a Galaxy environment variable for use within Tool Wrappers setting the number of threads/CPUs to use.
The idea is that you can configure a default value, and then override this per runner or per tool etc.
Thanks Peter for pushing this idea, I totally support this proposal. In the mean time, I've been using for my tools the solution by Jim Johnson for its CD-HIT wrapper:
http://toolshed.g2.bx.psu.edu/view/jjohnson/cdhit
But this requires the system administrator to modify both the tool env.sh and job_conf.xml to be in sync.
Is there an open Trello card for this?
A Trello card would be useful indeed.
Nicola
Better than a Trello card, we now have a pull request from John: https://bitbucket.org/galaxy/galaxy-central/pull-request/236/job-runner-enha...
And thanks to John its merged! Time for testing and migrating our tools :)
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 (e.g. on the cluster, when $GALAXY_SLOTS would be known). I have tried using \$GALAXY_SLOTS but it remains in the file generated by <configfile> as $GALAXY_SLOTS rather than being substituted. Thanks, Peter