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 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
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