On Thu, Jun 2, 2011 at 6:23 PM, Nate Coraor <nate(a)bx.psu.edu> wrote:
Peter Cock wrote:
> On a related point, I've previously suggested a $variable could be defined
> for use in tool XML wrappers to set the number of threads. This number
> could come from a general configuration file, or perhaps via the cluster
> settings - the point is the tool doesn't need to know, it just gets told how
> many threads it is allowed.
Yeah, that's the idea.
<destination name="default" runner="local"/>
<destination name="pbs_default" runner="pbs">
<tool id="upload1" destination="default"/>
<tool id="bowtie_wrapper" destination="pbs_default">
pbs.py then knows to translate '<resource
Your tool can access that value a bunch, like $__resources__.cores.
The same should be possible for other consumables.
Sounds good. Would there be a global default setting somewhere in
universe.ini or elsewhere for when job_conf.xml didn't set a value?