Difference between revisions of "Galaxy Configuration - Running Jobs"

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(Created page with "Category:Galaxy Configuration * job_conf.xml {{#fileAnchor: job_conf.xml}} Download raw source of the [{{#fileLink: job_conf.xml}} job_conf.xml] file. <source lang=xml> <?...")
 
 
(One intermediate revision by the same user not shown)
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[[Category:Galaxy Configuration]]
+
[[Category:Galaxy]]
 
* job_conf.xml
 
* job_conf.xml
 
{{#fileAnchor: job_conf.xml}}
 
{{#fileAnchor: job_conf.xml}}
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     <plugins workers="5">
 
     <plugins workers="5">
 
         <!-- "workers" is the number of threads for the runner's work queue.
 
         <!-- "workers" is the number of threads for the runner's work queue.
             The default from <plugins> is used if not defined for a <plugin>.
+
             The default from <plugins> is used if not defined for a <plugin>. -->
          -->
 
          <!--        <plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /> -->
 
 
         <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
 
         <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
 
         <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
 
         <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
        <!--        <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner"/> -->
 
 
     </plugins>
 
     </plugins>
 
     <handlers default="handlers">
 
     <handlers default="handlers">
         <!-- Additional job handlers - the id should match the name of a
+
         <!-- Additional job handlers - the id should match the name of a [server:<id>] in universe_wsgi.ini. -->
            [server:<id>] in universe_wsgi.ini.
 
        -->
 
 
         <handler id="handler0" tags="handlers"/>
 
         <handler id="handler0" tags="handlers"/>
 
         <handler id="handler1" tags="handlers"/>
 
         <handler id="handler1" tags="handlers"/>
        <!--
 
        <handler id="handler2" tags="handlers"/>
 
        -->
 
        <!--
 
        <handler id="special_handler0" tags="special_handlers"/>
 
        <handler id="special_handler1" tags="special_handlers"/>
 
        <handler id="trackster_handler"/>
 
        -->
 
 
     </handlers>
 
     </handlers>
 
     <destinations default="dynamic">
 
     <destinations default="dynamic">
Line 40: Line 27:
 
         </destination>
 
         </destination>
 
         <destination id="moab" runner="drmaa" />
 
         <destination id="moab" runner="drmaa" />
            <!-- TODO: The real user options should maybe not be considered runner params. -->
 
            <!--
 
            <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.sh</param>
 
            <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.sh</param>
 
            <param id="galaxy_external_chown_script">scripts/external_chown_script.sh</param>
 
            -->
 
            <!--            <destination id="torque" runner="pbs" /> -->
 
 
         <destination id="local" runner="local" />
 
         <destination id="local" runner="local" />
        <!--        <destination id="qsub" runner="cli">
+
    </destinations>
            <param id="job_plugin">Torque</param>
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    <tools>
        </destination>
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    </tools>
        -->
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    <limits>
         <!--
+
         <!-- Certain limits can be defined. -->
        <destination id="ssh_torque" runner="cli">
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    </limits>
            <param id="shell_plugin">SecureShell</param>
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</job_conf>
            <param id="job_plugin">Torque</param>
 
            <param id="shell_username">foo</param>
 
            <param id="shell_hostname">foo.example.org</param>
 
            <param id="Job_Execution_Time">24:00:00</param>
 
        </destination>
 
 
</source>
 
</source>

Latest revision as of 18:52, 7 July 2017

  • job_conf.xml

{{#fileAnchor: job_conf.xml}} Download raw source of the [{{#fileLink: job_conf.xml}} job_conf.xml] file.

<?xml version="1.0"?>
<job_conf>
    <plugins workers="5">
        <!-- "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="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
    </plugins>
    <handlers default="handlers">
        <!-- Additional job handlers - the id should match the name of a [server:<id>] in universe_wsgi.ini. -->
        <handler id="handler0" tags="handlers"/>
        <handler id="handler1" tags="handlers"/>
    </handlers>
    <destinations default="dynamic">
        <!-- Destinations define details about remote resources and how jobs
             should be executed on those remote resources. -->
        <destination id="local" runner="local" tags="head"/>
        <destination id="dynamic" runner="dynamic">
            <!-- A destination that represents a method in the dynamic runner. -->
            <param id="function">default</param>
            <param id="type">python</param>
        </destination>
        <destination id="moab" runner="drmaa" />
        <destination id="local" runner="local" />
    </destinations>
    <tools>
    </tools>
    <limits>
        <!-- Certain limits can be defined. -->
    </limits>
</job_conf>