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
<
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb...
<plugins> 2
<
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb...
<plugin id="pbs" type="runner"
load="galaxy.jobs.runners.pbs:PBSJobRunner"/> 3
<
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb...
</plugins> 4
<
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb...
<destinations default="pbs_default"> 5
<
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb...
<destination id="pbs_default" runner="pbs"/> 6
<
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb...
<destination id="other_cluster" runner="pbs"> 7
<
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb...
<param id="destination">(a)other.cluster</param> 8
<
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb...
</destination> 9
<
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb...
<destination id="long_jobs" runner="pbs"> 10
<
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb...
<param
id="Resource_List">walltime=72:00:00,nodes=1:ppn=8</param>
11
<
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb...
<param id="-p">128</param> 12
<
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb...
</destination> 13
<
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#CA-e4c8fb...
</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!
Thanks!
Rui