On Thu, 2 Jun 2011 13:31:04 -0400, Nate Coraor <n...@bx.psu.edu> wrote: > Peter Cock wrote: >> On Thu, Jun 2, 2011 at 6:23 PM, Nate Coraor <n...@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. >> > >> > 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 .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? > > default_cluster_job_runner will remain for backwards compatibility, but > we'll ship a sample job_conf.xml that runs everything locally by > default. > > --nate
Haha, and I did that before realizing I could do just what I needed by writing tool-specific pbs:// URLs at the end of the config file... I'm such an idiot. But I really like what you did of it and I have a couple of questions. Concerning the single-threaded tools, what would happen if the number of threads set in the xml file was >1 ? Could it be possible to forbid a tool to run on a given node? Thanks, L-A > >> >> Peter >> ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
