Installing Metavisitor with Docker

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We distribute a docker image of Metavisitor, which can thus be used to run a Metavisitor docker container. For a quick start, go directly to the last section "Persisting to disk".

Requirements

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

Running images from the dockerhub

You can search for pre-built docker images from the dockerhub by typing in the terminal of the machine where you want to run the docker container:

docker search metavisitor

Then, to get the docker image, type:

docker pull artbio/metavisitor-2

In this documentation, we recommend to use the artbio/metavisitor-2 which better corresponds to the environment described in our Metavisitor preprint

When this pull is done (may take a few minutes depending on your connection speed to the dockerhub), you can start the container by typing:

docker run -d -p 80:80 artbio/metavisitor-2

This command starts a container in daemon mode (-d) from the image and serve it on port 80 of the local machine in the standard docker way.

-p 80:80 forwards requests to nginx inside the container running on port 80. If you want to access the machine hosting the running container through another port (for instance 8080), just change -p 80:80 to -p 8080:80

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.

For instance,

docker run -d -e NGINX_GALAXY_LOCATION="/my-subdirectory" -p 80:80 artbio/metavisitor-2

will get the metavisitor docker container serving at http://127.0.0.1:80/my-subdirectory.

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

docker run -d -e NGINX_GALAXY_LOCATION="/my-subdirectory" -e GALAXY_CONFIG_ADMIN_USERS=admin@artbio.fr -p 80:80 artbio/galaxy-kickstart-base

Note that if you do not make this latest change, the admin login for the metavisitor container is by default admin@galaxy.org and the password is admin.

Persisting to disk

All changes made to a docker container are by default ephemeral; if you remove the container, the changes are gone. To persist data (this includes the postgresql database, galaxy's config files and your user 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. Thus, assuming you would like to mount your local /my/data folder and persist you Galaxy data in this folder, run

docker run -d --privileged -v /my/data:/export -p 80:80 artbio/metavisitor-2

This will run through the persistence tags of the galaxy.yml and export the required files to /export (now on your machine's /my/data). From the new location the files are being bind-mounted back into their original location.