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galaxy-hackathon-2014
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galaxy-hackathon-2014
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Integrating Docker-based tools within Galaxy ============================================ This document describes a method for integrating [Docker](http://www.docker.com/) based tools within [Galaxy](http://galaxyproject.org/). Docker is a method for wrapping up a tool along with all of it's dependencies into a single container which can be distrubted with the help of [Dockerhub](https://hub.docker.com/). A method to run docker based tools was added to Galaxy in https://bitbucket.org/galaxy/galaxy-central/pull-request/401/allow-tools-and-deployers-to-specify/diff. Initial Galaxy and Docker Setup ------------------------------- ### Setup Latest Galaxy Please download and setup the latest Galaxy from galaxy-central. More detailed instructions are found at https://wiki.galaxyproject.org/Admin/GetGalaxy but the two main commands you need to run are: ```bash $ hg clone https://bitbucket.org/galaxy/galaxy-central $ cd galaxy-central $ sh run.sh ``` ### Setup Docker Test Tool A test tool configuration file `catDocker.xml` is included with Galaxy (or at [catDocker.xml](catDocker.xml)). This can be setup with the following commands (run within `galaxy-central` directory). 1. Setup `catDocker.xml` tool ```bash $ mkdir tools/docker $ cp test/functional/tools/catDocker.xml tools/docker/ ``` Now, in the `tool_conf.xml` file please add a new section for this tool: ```xml <section> <tool file="docker/catDocker.xml"/> </section> ``` 2. Construct a `job_conf.xml` which instructs Galaxy to run tools docker-based tools using docker. Construct a basic `job_conf.xml` with the following command. ```bash cp job_conf.xml.sample_basic job_conf.xml ``` Add a docker destination in `job_conf.xml` to enable running through docker: ```xml <destinations default="docker_local"> <destination id="local" runner="local"/> <destination id="docker_local" runner="local"> <param id="docker_enabled">true</param> </destination> </destinations> ``` More information can be found in the `job_conf.xml.sample_advanced` file that comes with Galaxy. 3. Enable docker to run using sudo without a password. Add docker runner to sudoers file (replace `galaxy` with the username you are running galaxy under): ``` galaxy ALL = (root) NOPASSWD: SETENV: /usr/bin/docker ``` 4. Start up Galaxy ```bash $ sh run.sh ``` 5. Test Run test tool **Concatenate datasets (in docker)** Check log file. If the tool ran you should see entries with `docker` like: ``` command is: sudo docker run -e "GALAXY_SLOTS=$GALAXY_SLOTS" -v /home/aaron/Projects/galaxy-central:/home/aaron/Proje cts/galaxy-central:ro -v /home/aaron/Projects/galaxy-central/tools/docker:/home/aaron/Projects/galaxy-central/tools/docker:ro -v /home/aaron/Projects/galaxy-central/datab ase/job_working_directory/000/6:/home/aaron/Projects/galaxy-central/database/job_working_directory/000/6:rw -v /home/aaron/Projects/galaxy-central/database/files:/home/aa ron/Projects/galaxy-central/database/files:rw -w /home/aaron/Projects/galaxy-central/database/job_working_directory/000/6 --net none busybox:ubuntu-14.04 /home/aaron/Projects/galaxy-central/database/job_working_directory/000/6/container.sh; return_code=$?; if [ -f /home/aaron/Projects/galaxy-central/database/job_working_directory/000/6/wo rking_file ] ; then cp /home/aaron/Projects/galaxy-central/database/job_working_directory/000/6/working_file /home/aaron/Projects/galaxy-central/database/files/000/dataset_10.dat ; fi; sh -c "exit $return_code" ``` Integrating SMALT with Docker ----------------------------- This contains information on how to integrated a more complicated tool (SMALT) with Docker. Please see documentation at [SMALT+Docker](smalt/).
