Peter Cock wrote:
2011/6/2 Nate Coraor <nate@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