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Galaxy ConfigurationΒΆ

This page is for notes on UFRC Galaxy instance configuration, which may be useful to others trying to set up their own Galaxy.

List of the issues with the UF Galaxy that we are aware of and are actively working on or have them in the queue to address later. Some of these issues are due to the the bugs in the Galaxy code provided by the Galaxy Team. Others are UF Galaxy specific. Please check this page before submitting a new support request ticket.

2013-01-31:

  • Uploading a composite "lped" dataset type is broken when jobs are run under a real user id. The core team is working on addressing the issue.

  • 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>