Cool stuff the Ensembl VEP can do: install using Docker

We know that installing the VEP is not always trivial – there are dependencies and modules that you may or may not have already, and your existing setup may require different module versions. It’s also designed for a Linux system and installing on, for example, Windows, can be complex. To get around this, the VEP and all its dependencies are available in a Docker image, so that you can install everything with just a few simple commands.

Docker is a platform that allows software to be delivered in containers, instead of as standalone applications. This means that instead of installing and setting up a piece of software, then doing the same with a bunch of other software that you need to make it run, you can install one container, which has all this stuff in it, all ready to go.

For VEP, we have a container set up with the VEP itself plus all its dependencies. Since the VEP is already installed in the container, there is no need to run the installation script, so we’ve actually removed some of the files needed for this from the container to make it more lightweight.

To use the VEP Docker image, you first need to install Docker, then you can pull in the VEP and set it up in a few easy steps. If you need caches and plugins, you can do this in Docker too with a reduced version of the installation script.