Adding software to an image

When you create a biobox image you'll want to add your own bioinformatics software and the any third-party dependencies it needs. This guide illustrates how to install and include software in an image.

Installing using apt

A relatively simple way to install any software you require is using the advanced packaging tool (apt). Apt is used by an Ubuntu or Debian Linux image, so we'll need to switch to using one of these as the base image. Docker recommends Debian as the base image, because it's small and well-maintained.

FROM debian:stable

Notice here you can specify different versions of an operating system by adding a tag after the name using a colon (:). In this case we use the stable version of Debian. Take a look at the Debian page on DockerHub and you can see that there are a large number of tags available. Build and then log into this image.

docker build --tag apt_image .
docker run --interactive --tty apt_image /bin/bash

Apt allows you to install packages relatively easily as long as you know their name. First though you'll need to update the list of packages apt uses. Do this using apt-get update.

apt-get update

This will stream some text as apt fetches all available packages that can be installed. For this guide we'll install the velvet genome assembler, one of the early short read assemblers. To do this we'll need to search through the list of available packages.

apt-cache search velvet

This will return a list of apt packages that match the name 'velvet'. The first one is the velvet assembler, so that's the one we'll install.

apt-get install velvet

You can ensure that velvet is installed and available after doing this by running the command velveth which lists the command line options for running velvet. Now exit the container by pressing CTRL+D.

Installing with the Dockerfile

When you build an image you would install velvet automatically. This can be done using the RUN directive which executes the given commands as the image is being built. In this case we'll add the commands we used to install velvet. We'll combine them using && which means 'run the second command if the first one works'. We also add --yes which skips the prompt asking about installing the software.

FROM debian:stable

RUN apt-get update && apt-get install --yes velvet

Build this image and you'll see the output of apt installing velvet. If you log into this image and run velveth again, you'll see velvet is installed.

docker build --tag velvet .