Hi,
I am struggling to get galaxy to submit job to a cluster, I am using Torque
and Maui.
This is my universe_wsgi.ini
----- Handler Definitions
-------------------------------------------------
[server:web0]
use = egg:Paste#http
port = 8181
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 7
[server:web1]
use = egg:Paste#http
port = 8182
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 7
[server:handler0]
use = egg:Paste#http
port = 8090
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5
[server:handler1]
use = egg:Paste#http
port = 8091
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5
# ------ Handler Definitions
-------------------------------------------------
This is job_conf.xml
*<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way it
is configured by default (if there is no explicit config). -->
<job_conf>
<plugins workers="4">
<plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
<plugin id="pbs" type="runner"
load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="6"/>
</plugins>
<handlers default="handlers">
<handler id="handler0" tags="handlers"/>
<handler id="handler1" tags="handlers"/>
</handlers>
<destinations default="regularjobs">
<destination id="local" runner="local"/>
<destination id="regularjobs" runner="pbs" tags="cluster">
<param id="Resource_List">walltime=24:00:00</param>
<param
id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>
<param
id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>
<param
id="galaxy_external_chown_script">scripts/external_chown_script.py</param>
</destination>
<destination id="real_user_cluster" runner="pbs">
<param
id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>
<param
id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>
<param
id="galaxy_external_chown_script">scripts/external_chown_script.py</param>
</destination>
<destination id="dynamic" runner="dynamic">
<!-- A destination that represents a method in the dynamic
runner. -->
<param id="type">python</param>
<param id="function">interactiveOrCluster</param>
</destination>
</destinations>
</job_conf><?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way it
is configured by default (if there is no explicit config). -->
<job_conf>
<plugins workers="4">
<plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
<plugin id="pbs" type="runner"
load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="6"/>
</plugins>
<handlers default="handlers">
<handler id="handler0" tags="handlers"/>
<handler id="handler1" tags="handlers"/>
</handlers>
<destinations default="regularjobs">
<destination id="local" runner="local"/>
<destination id="regularjobs" runner="pbs" tags="cluster">
<param id="Resource_List">walltime=24:00:00</param>
<param
id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>
<param
id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>
<param
id="galaxy_external_chown_script">scripts/external_chown_script.py</param>
</destination>
<destination id="real_user_cluster" runner="pbs">
<param
id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>
<param
id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>
<param
id="galaxy_external_chown_script">scripts/external_chown_script.py</param>
</destination>
<destination id="dynamic" runner="dynamic">
<!-- A destination that represents a method in the dynamic
runner. -->
<param id="type">python</param>
<param id="function">interactiveOrCluster</param>
</destination>
</destinations>
</job_conf>*
I can submit jobs to the cluster so I know that part is working. Any help
would be appreciated.
--
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет
Jurgens de Bruin