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"?>


    <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"/>


    <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"/>



    <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 id="longjobs" runner="pbs" tags="cluster,long_jobs">

            <!-- These are the parameters for qsub, such as queue etc. -->


        <destination id="shortjobs" runner="pbs" tags="cluster,short_jobs">

            <!-- These are the parameters for qsub, such as queue etc. -->


        <destination id="multicorejobs" runner="pbs" tags="cluster,multicore_jobs">

            <!-- These are the parameters for qsub, such as queue etc. -->


       <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 id="dynamic" runner="dynamic">

            <!-- A destination that represents a method in the dynamic runner. -->

            <param id="type">python</param>

            <param id="function">interactiveOrCluster</param>




        <!-- 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"/>



        <!-- 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>