On Thu, Oct 24, 2013 at 5:53 PM, James Taylor <james(a)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 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,
Peter