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.