Destination Parameters not being passed

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1

Hi,

We have Galaxy hooked into a cluster using Torque as the scheduler. I’ve setup a second destination for specific tools to call more resources (nodes=1:ppn=14). The jobs go through, but the resource call is not being used.

Snip from job_conf.xml:

    <destinations default="torque_default">
    <destination id="local" runner="local"/>
    <destination id="multicore_local" runner="local">
        <param id="local_slots">4</param> <!-- Specify GALAXY_SLOTS for local jobs. -->
        <!-- Warning: Local slot count doesn't tie up additional worker threads, to prevent over
           allocating machine define a second local runner with different name and fewer workers
           to run this destination. -->
        <param id="embed_metadata_in_job">True</param>
        <!-- Above parameter will be default (with no option to set
           to False) in an upcoming release of Galaxy, but you can
           try it early - it will slightly speed up local jobs by
           embedding metadata calculation in job script itself.
        -->
        <job_metrics />
        <!-- Above element demonstrates embedded job metrics definition - see
           job_metrics_conf.xml.sample for full documentation on possible nested
           elements. This empty block will simply disable job metrics for the
           corresponding destination. -->
    </destination>
    <destination id="torque_default" runner="pbs"/>
        <param id="Resource_List">nodes=1:ppn=1</param>
    <destination id="torque_whole" runner="pbs"/>
        <param id="Resource_List">nodes=1:ppn=14</param>
    <destination id="ssh_torque" runner="cli">
        <param id="shell_plugin">SecureShell</param>
        <param id="job_plugin">Torque</param>
        <param id="shell_username">fbgalaxy</param>
        <param id="shell_hostname">fb-image-compute01</param>
    </destination>
</destinations>

<tools>
    <!-- <tool id="nia_hmm" destination="multicore_local"/>    
    <tool id="sid_mito_analysis" destination="multicore_local"/>   -->
    <tool id="correct_bg_versions" destination="torque_whole"/>
    <tool id="correct_bg_versions_dev" destination="torque_whole"/>
    <tool id="montage_versions" destination="torque_whole"/>
    <tool id="montage_versions_dev" destination="torque_whole"/>
    <tool id="variety_alignments" destination="torque_whole"/>
    <tool id="variety_alignments_dev" destination="torque_whole"/>
</tools>
2

:man_facepalming:

I had my closing bracket before the parameters.

My destination block now looks like:

<destination id="torque_default" runner="pbs">
    <param id="Resource_List">nodes=1:ppn=1</param>
</destination>
<destination id="torque_whole" runner="pbs">
    <param id="Resource_List">nodes=1:ppn=14</param>
</destination>