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