Re: [galaxy-user] suggestion for multithreading

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.