Building and deploying galaxy-kickstart in docker¶

Requirements¶

You need to have docker installed and configured for your user.

The repository comes with a Dockerfile that can be used to build a Docker image. This image is already available at hub.docker.com and can be pulled using the command docker pull artbio/galaxykickstart:18.04.

Building a GalaxyKickstart Docker image¶

If you wish to adapt GalaxyKickStart to build a Docker image adapted to your needs, you will have to customise the Dockerfile (Dockerfile.galaxykickstart-base) by updating the inventory file inventory_files/docker and its dependencies group_vars/docker and extra-files/docker/. Then, run the following command:

docker build -t mygalaxykickstart .

Running the available docker image from the dockerhub¶

Pull the docker image:

docker pull artbio/galaxykickstart:18.04

Start the image and serve it on port 8080 of your local machine in the standard docker way:

CID=`docker run -d -p 8080:80 artbio/galaxykickstart:18.04`

-p 8080:80 will forward requests to nginx inside the container running on port 80.

Runtime changes to pre-built docker images¶

If you wish to reach the container on a subdirectory, add -e NGINX_GALAXY_LOCATION="/my-subdirectory" to the docker call and galaxy will be served at http://127.0.0.1:8080/my-subdirectory.

We recommend changing the default admin user as well, so the command becomes:

CID=`docker run -d -e NGINX_GALAXY_LOCATION="/my-subdirectory" \
     -e GALAXY_CONFIG_ADMIN_USERS=admin@artbio.fr \
     -p 8080:80 artbio/galaxykickstart:18.04`

Commit changed containers to new images¶

As with standard docker containers, you can change, tag and commit running containers when you have configured them to your likings.

Commit the changes to my-new-image:

docker commit $CID my-new-image

Stop and remove the original container:

docker stop $CID && docker rm $CID

Start the new container:

CID=`docker run -d -e NGINX_GALAXY_LOCATION="/my-subdirectory" \
     -e GALAXY_CONFIG_ADMIN_USERS=admin@artbio.fr \
     -p 8080:80 my-new-image`

Persisting to disk¶

All changes made to the container are by default ephemeral. If you remove the container, the changes are gone. To persist data, including the postgresql database, galaxy's config files and your user galaxy data, mount a Volume into the containers /export folder. Due to the persistance mechanism (we use bind-mounts inside the container), you need to privilege the container. Assuming you would like to mount your local /data folder, run

CID=`docker run -d --privileged \
     -v /data:/export \
     -p 8080:80
     artbio/galaxykickstart:18.04`

This will run through the persistence tags of the galaxy.yml and export the required files to /export (now on your machine's /data).

From the new location the files are being bind-mounted back into their original location.