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Files in this repository are a Dockerized version of the
Galaxy 101 toolset.

To use the contents of this repository, relevant tools need to be added
to a given Galaxy instance. To do so, place the tool wrappers (ie,
XML files; see download_wrappers.sh) into $GALAXY_HOME/tools/docker/ and
edit $GALAXY_HOME/config/tool_conf.xml to include those tools, for example:

<section id="galaxy101d" name="Dockerized Galaxy 101 tools">
    <tool file="docker/join.xml"/>
    <tool file="docker/grouping.xml"/>
    <tool file="docker/sorter.xml"/>
    <tool file="docker/headWrapper.xml"/>
    <tool file="docker/compare.xml"/>
</section>

Some tool wrappers exist in the Galaxy source code distribution and are thus
included with Galaxy instances by default but do not specify a wrapper version.
This manifests itself with Galaxy not being able to distinguish between multiple
wrapper versions. As a workaround, to have the Docker tools load in the tool
panel without removing the distribution tools from tool_conf.xml, place the
Docker tool section at the bottom of the tool_conf.xml file.

Next, it is necessary to tell Galaxy to enable Docker when running tools. This
is done in config/job_conf.xml by specifying
<param id="docker_enabled">true</param> on the desired destination. For
example, if targerting a Pulsar server, the following configuration
is necessary:

<?xml version="1.0"?>
<job_conf>
    <plugins>
        ...
        <plugin id="pulsar_rest" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner" />
        ...
    </plugins>
    <handlers default="main">
        <handler id="main" />
    </handlers>
    <destinations default="pulsar_server">
        ...
        <destination id="pulsar_server" runner="pulsar_rest">
            <param id="docker_enabled">true</param>
            <param id="docker_set_user">[galaxy_user_uid (eg, 1001 for CloudMan)]</param>
            <param id="url">http://[pulsar_server_ip]:[pulsar_server_port]/</param>
        </destination>
        ...
    </destinations>
</job_conf>

Then, restart the Galaxy instance and the tools will be available. Note that
the machine running these tools' jobs needs to be able to actually run Docker
containers (ie, have Linux kernel version 3.8+).
Also note that the Join tool requires operation_filter.py to be made
available in the same directory as the tool's XML file (ie, join.xml).

A Docker image with these tools is available on the Docker Hub.

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afgane
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