Hi everyone´╝î
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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