On Thu, Oct 24, 2013 at 5:53 PM, James Taylor email@example.com 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 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).
Unfortunately, the former, and there is no easy way to change this.
Ah. That was what I suspected :(
One could do some simple variable substitution on the config file when the job runs though (sed would do the job here, not pretty but it works).
Yeah - I was thinking about something like that as a work around, although since I have a wrapper Python script anyway I can do the edit there: https://github.com/peterjc/pico_galaxy/tree/master/tools/mira4
Thanks for such a prompt answer,