Core Docker commands

$ docker login pgc-images.sbgenomics.com

This returns a prompt for your CAVATICA credentials, and then, if satisfied, gives you access to the CAVATICA registry. Don't forget to add pgc-images.sbgenomics.com to this command, or else the utility will attempt to log you in to the Docker Hub registry.

$ docker run -ti <image>

This runs a Docker container on your local machine. <image> can be any image in Docker Hub or the CAVATICA image registry that you have uploaded or have permission to access. The -ti flag makes the container run, interactively.

If you are opening an image from Docker Hub, specify <image> using <docker_repository>[:tag], e.g. ubuntu.
If you are opening an image from the CAVATICA registry, <image> should be specified using the format pgc-images.sbgenomics.com/<username>/<repository_name>/[:tag], e.g pgc-images.sbgenomics.com/rfranklin/samtools:v1.

$ docker ps -a

This lists all your Docker containers.

docker commit <container ID> pgc-images.sbgenomics.com/<username>/<repository_name>[:tag]

This takes an image (snapshot) of the container with ID <container ID>, and names the image with the format recognised by the CAVATICA registry.
You can find the container ID of an image using docker ps -a.

$ docker images

This lists all your local Docker images.

$ docker tag <image> pgc-images.sbgenomics.com/<username>/<repository_name>[:tag]

This tags the image with a reference to
the CAVATICA registry.

$ docker push pgc-images.sbgenomics.com/<username>/<repository_name>[:tag]

This uploads your Docker image to the CAVATICA registry, so that the tool in it can be used on CAVATICA.

$ docker rmi pgc-images.sbgenomics.com/<username>/<repository_name>[:tag]

This removes the specified Docker image from your local machine

$ docker pull pgc-images.sbgenomics.com/<username>/<repository_name>[:tag]

This downloads the specified image from the CAVATICA registry.

$ docker logout pgc-images.sbgenomics.com

This stops your connection to the CAVATICA image registry.