Re: [galaxy-user] suggestion for multithreading

On Thu, Jun 2, 2011 at 6:23 PM, Nate Coraor <nate(a)bx.psu.edu&gt; 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. > > job_conf.xml: > > <?xml version="1.0"?> > <job_conf> >    <destinations> >        <destination name="default" runner="local"/> >        <destination name="pbs_default" runner="pbs"> >            <native_param name="queue">batch</native_param> >        </destination> >    </destinations> >    <tools> >        <tool id="upload1" destination="default"/> >        <tool id="bowtie_wrapper" destination="pbs_default"> >            <resource type="cores">8</resource> >        </tool> >    </tools> > </job_conf> > > pbs.py then knows to translate '<resource type="cores">8</resource>' to > '-l nodes=1:ppn=8'. > > 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?

Peter