Peter Cock wrote:
> 2011/6/2 Nate Coraor <n...@bx.psu.edu>:
> > Hi Louise-Amélie,
> >
> > I haven't done anything with this code yet, but I wanted to let you know
> > that we'll eventually be adding it, I'm just going to change the
> > implementation slightly.  I'd like to merge the functionality of the csv
> > into an xml config I'm already working on (but haven't yet fully decided
> > on the syntax).  And it should be possible for tools to access these
> > parameters in the command line template.  A lot of our NGS tools have
> > the number of threads to use hardcoded in the tool config, which is bad.
> >
> > --nate
> 
> 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.

--nate

> 
> Peter
> 
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