Reproducible computational environments using containers

Almost all software depends on other software components to function, but these components have independent evolutionary paths.

Projects involving many software components can rapidly run into a combinatoric explosion in the number of software version configurations available, yet only a subset of possible configurations actually works as desired.

Containers collect software components together and can help avoid software dependency problems.

Virtualisation is an old technology that container technology makes more practical.

Docker is just one software platform that can create containers and the resources they use.

A toolbar icon indicates that Docker is ready to use.

You will typically interact with Docker using the command line.

Containers are usually created using command line invocations.

The docker run command creates containers from images.

The docker image command can list and manage images that are (now) on your computer.

The docker container command can list and manage containers that have been created.

The -d -t options to docker run allow you to create a container running in the background.

The docker exec command allows you to execute commands in a running container, including getting interactive access.

The Docker Hub is an online repository of container images.

Many Docker Hub images are public, and may be officially endorsed.

Each Docker Hub page about an image provides structured information and subheadings

Most Docker Hub pages about images contain sections that provide examples of how to use those images.

Dockerfiles specify what is within Docker images.

The docker build command is used to build an image from a Dockerfile

You can share your Docker images through the Docker Hub so that others can create Docker containers from your images.

You can include files from your Docker host into your Docker images by using the COPY instruction in your Dockerfile.

Docker allows containers to read and write files from the Docker host.

You can export and import images from files.

By using the container we avoid all the difficult installation issues of installing Jekyll.

Container images allow us to encapsulate the computation (and data) we have used in our research.

Using a service such as Docker Hub allows us to easily share computational work we have done.

Using container images along with a DOI service such as Zenodo allows us to capture our work and enables reproducibility.