afgane/galaxy101 repository overview

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>

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.