Hi everyone，
I am a newer in Galaxy. I installed my Galaxy with Torque2.5.0 . I used my
job_conf.xml for a test ,my Galaxy seems to work with TORQUE by the interface
of pbs_modoule ( _pbs.so) successfully.
In my test job_conf.xml , it seems that we should use <tools>collection of
<tool id="bwa_wrapper" destination="multicorejobs4"/>to specify bwa to run as
multicorejobs4. But I do not sure wheather all the tools in Galaxy we should
specify their destination (such as, regularjobs,longjobs), or all the tools
would work with a default destination(<destinations
default="regularjobs">).,unless we specify them.
Could anyone give me some help please?
This is my test job_conf.xml:
<?xml version="1.0"?>
<job_conf>
<plugins workers="4">
<!-- "workers" is the number of threads for the runner's work queue.
The default from <plugins> is used if not defined for a
<plugin>.-->
<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="8"/>
</plugins>
<handlers default="batch">
<!-- Additional job handlers - the id should match the name of a
[server:<id>] in universe_wsgi.ini. -->
<handler id="node01" tags="batch"/>
<handler id="node02" tags="batch"/>
<!-- <handler id="handler10" tags="handlers"/>
<handler id="handler11" tags="handlers"/>
<handler id="handler12" tags="handlers"/>
<handler id="handler13" tags="handlers"/>
-->
</handlers>
<destinations default="regularjobs">
<!-- Destinations define details about remote resources and how jobs
should be executed on those remote resources. -->
<destination id="local" runner="local"/>
<destination id="regularjobs" runner="pbs" tags="cluster">
<!-- These are the parameters for qsub, such as queue etc. -->
</destination>
<destination id="longjobs" runner="pbs" tags="cluster,long_jobs">
<!-- These are the parameters for qsub, such as queue etc. -->
</destination>
<destination id="shortjobs" runner="pbs" tags="cluster,short_jobs">
<!-- These are the parameters for qsub, such as queue etc. -->
</destination>
<destination id="multicorejobs" runner="pbs"
tags="cluster,multicore_jobs">
<!-- These are the parameters for qsub, such as queue etc. -->
</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>
<tools>
<!-- Tools can be configured to use specific destinations or handlers,
identified by either the "id" or "tags" attribute. If assigned to
a tag, a handler or destination that matches that tag will be
chosen at random.-->
<tool id="bwa_wrapper" destination="multicorejobs"/>
</tools>
<limits>
<!-- Certain limits can be defined.-->
<limit type="registered_user_concurrent_jobs">500</limit>
<limit type="unregistered_user_concurrent_jobs">1</limit>
<limit type="concurrent_jobs" id="local">1</limit>
<limit type="concurrent_jobs" tag="cluster">200</limit>
<limit type="concurrent_jobs" tag="long_jobs">200</limit>
<limit type="concurrent_jobs" tag="short_jobs">200</limit>
<limit type="concurrent_jobs" tag="multicore_jobs">100</limit>
</limits>
</job_conf>
shenwiyn
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