On Fri, Apr 17, 2015 at 3:26 PM, Beginner TI <ruiwang...@gmail.com> wrote: > Hi, > > I'm trying to enable the capability to submit jobs to a pbs cluster, however > I am quite confused by the documentation. I don't know where I could specify > the pbs server. I saw the following on the page: > > https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster > > > 1 <plugins> > 2 <plugin id="pbs" type="runner" > load="galaxy.jobs.runners.pbs:PBSJobRunner"/> > 3 </plugins> > 4 <destinations default="pbs_default"> > 5 <destination id="pbs_default" runner="pbs"/> > 6 <destination id="other_cluster" runner="pbs"> > 7 <param id="destination">@other.cluster</param> > 8 </destination> > 9 <destination id="long_jobs" runner="pbs"> > 10 <param > id="Resource_List">walltime=72:00:00,nodes=1:ppn=8</param> > 11 <param id="-p">128</param> > 12 </destination> > 13 </destinations> > > > is this <param id="destination"> the place you specify where your pbs/torque > server? and the syntax is to prepend a '@' to the server name? for example, > should a most basic config look like: > > <plugins> > <plugin id="pbs" type="runner" > load="galaxy.jobs.runners.pbs:PBSJobRunner"> > </plugins> > <destinations default="pbs"> > <destination id="pbs" runner="pbs" > > <param id="destination">@pbs_server_full_name</param> > <param > id="Resource_List">walltime=72:00:00,nodes=1:ppn=8</param> > <param id="-q">myqueue</param> > </destination> > <destinations> > > I searched online and to my surprise I didn't find any useful information, > or any working sample...please give me a hand guys!
I think destination just maps to the qsub -q parameter - so whatever you would fill in there on the command line you can just place in the destination argument. I really am unsure if the @ is needed - but can you try to experiment on the command line and find the right target with qsub and then just fill that value into job_conf.xml? -John > > Thanks! > Rui > > > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
