Enable Galaxy to use BioContainers (Docker)

This is a very cool feature where Galaxy automatically detects that your tool has an associated docker image, pulls it and runs it for you. These images (when available) have been generated using mulled . To test, install the IUC bedtools from the toolshed. When you try to execute ClusterBed for example. You may get a missing dependancy error for bedtools . But bedtools has an associated docker image on quay.io . Now configure Galaxy as follows:

• Add this environment variable to docker run : -e GALAXY_CONFIG_ENABLE_MULLED_CONTAINERS=True
• In job_conf.xml configure a Docker enabled destination as follows:

<destination id="docker_local" runner="local">
    <param id="docker_enabled">true</param>
    <param id="docker_volumes">$galaxy_root:ro,$galaxy_root/database/tmp:rw,$tool_directory:ro,$job_directory:ro,$working_directory:rw,$default_file_path:rw</param>
    <param id="docker_sudo">false</param>
</destination>

When you execute the tool again, Galaxy will pull the image from Biocontainers ( quay.io/biocontainers ), run the tool inside of this container to produce the desired output.