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Galaxy InteractiveTools

Galaxy Interactive Tools allows launching a container-backed Galaxy Tool and enabling a Galaxy User to gain access to content inside in real-time.

How Galaxy InteractiveTools work

A InteractiveTool is defined in the same familiar way as standard Galaxy Tools, but are specified with tool_type=”interactive”, and providing additional entry point information:

<entry_points>
    <entry_point name="Display name">
        <port>80</port>
        <url><![CDATA[optional/path/can/be/${templated}]]></url>
    </entry_point>
</entry_points>

Note that name, port, and url are each able to be templated from the InteractiveTool’s parameter dictionary.

Some important benefits of using Galaxy InteractiveTools

  • You can have and access any number of InteractiveTools at a time (admin configurable)
  • If you accidentally close the InteractiveTool browser window, you can regain access by selecting from a list of active InteractiveTools
  • A single InteractiveTool can grant access to multiple running applications, servers, and interfaces
  • InteractiveTools can be added to Galaxy Workflows
  • Native, out-of-the box support for InteractiveTools in Galaxy via uWSGI proxying
  • InteractiveTools are bonafide Galaxy Tools; just specify tool_type as “interactive” and list the ports you want to expose
  • InteractiveTools can be added to and installed from the ToolShed.
  • R Shiny apps, Javascript-based VNC access to desktop environments, genome-browsers-in-a-box, interactive notebook environments, etc, are all possible with InteractiveTools

Server-side configuration of Galaxy InteractiveTools

The galaxy.yml file will need to be populated as seen in config/galaxy.yml.interactivetools.

In the uwsgi: section:

http-raw-body: true
# master: true

interactivetools_map: database/interactivetools_map.sqlite
python-raw: scripts/interactivetools/key_type_token_mapping.py
route-host: ^([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)-([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.(interactivetool\.localhost:8080)$ goto:interactivetool
route-run: goto:endendend
route-label: interactivetool
route-host: ^([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)-([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.([A-Za-z0-9]+(?:-[A-Za-z0-9]+)*)\.(interactivetool\.localhost:8080)$ rpcvar:TARGET_HOST rtt_key_type_token_mapper_cached $1 $3 $2 $4 $0 5
route-if-not: empty:${TARGET_HOST} httpdumb:${TARGET_HOST}
route: .* break:404 Not Found
route-label: endendend

In the galaxy: section:

interactivetools_enable: true

The admin should modify the route-host**s and **interactivetools_prefix to match their preferred configuration.

An example job_conf.xml file as seen in config/job_conf.xml.interactivetools:

<job_conf>
    <plugins>
        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
    </plugins>
    <destinations default="docker_dispatch">
        <destination id="local" runner="local"/>
        <destination id="docker_local" runner="local">
          <param id="docker_enabled">true</param>
          <param id="docker_volumes">$galaxy_root:ro,$tool_directory:ro,$job_directory:rw,$working_directory:rw,$default_file_path:ro</param>
          <param id="docker_sudo">false</param>
          <param id="docker_net">bridge</param>
          <param id="docker_auto_rm">true</param>
          <param id="require_container">true</param>
        </destination>
        <destination id="docker_dispatch" runner="dynamic">
            <param id="type">docker_dispatch</param>
            <param id="docker_destination_id">docker_local</param>
            <param id="default_destination_id">local</param>
        </destination>
    </destinations>
</job_conf>

Alternatively to the local job runner, InteractiveTools have been enabled for the condor job runner, e.g.:

<destination id="condor" runner="condor">
    <param id="docker_enabled">true</param>
    <param id="docker_sudo">false</param>
</destination>

Note on resource consumption: Keep in mind that Distributed Resource Management (DRM) / cluster systems may have a maximum runtime configured for jobs. From the Galaxy point of view, such a container could run as long as the user desires, this may not be advisable and an admin may want to restrict the runtime of InteractiveTools (and jobs in general). However, if the job is killed by the DRM, the user is not informed beforehand and data in the container could be discarded.

Some example test InteractiveTools have been defined, and can be added to the config/tool_conf.xml:

<tool file="interactive/interactivetool_jupyter_notebook.xml" />
<tool file="interactive/interactivetool_cellxgene.xml" />