Open Science on INBO Tutorials

Containers (1): An Overview

Fri, 21 Feb 2025 00:00:00 +0000

You might have heard about “containerization” with Docker. Docker has been labeled “the Holy Grail of reproducibility” in The Open Science Manual by Claudio Zandonella Callegher and Davide Massidda (2023). Although containerization is an immensely useful Open Science tool worth striving for, the Holy Grail is an inaccurate metaphor, because

(i) Unlike The Grail, Docker is easy to find and accessible.
(ii) Docker alone does not make a reproducible workflow; some of its capability is occasionally confused with package version management.
(iii) Docker has issues, some of them mitigated by configuration adjustment or switching to “Podman”.

I could not resist generating^* a catchy image on this, just to make this tutorial seem a little less dull.

Time to explore what containers really are, and what they are not.

Containers (2): Running Existing Containers

Fri, 21 Feb 2025 00:00:00 +0000

Docker is about assembling and working in containers. “Living” in containers. Or, rather, you can think of this as living in a “tiny home”, or “mobile home”. (Let’s call it a fancy caravan.) In the simple, but comfortable case, you do not get to pick a general design or to choose all details of the interior: you just take that wheeled cabine “as is” from a tiny home reseller.

A tiny home close to "Gare Maritime", Brussels, February 2025.

Just as a tiny home is a mini-version of an immobile house, a container can be thought of as a miniature computer which can be transferred to other computing environments. The good news: there are a gazillion Docker images available on repositories like Docker Hub or Quay.

Containers (3): Building Custom Containers

Fri, 21 Feb 2025 00:00:00 +0000

By now, you will have successfully installed Docker or Podman. You hopefully succeeded in running others’ containers, e.g. from a container repository.

Next, it is time to customize your container.

To give you a metaphor to work on: imagine you have a nice little DIY project for your garage workshop. This time, you would like to build your own Matryoshka dolls (матрёшка, stacking dolls, a great allegory for recursion).

(Photo by Iza Gawrych on Unsplash)

Like all good DIY, you do not fully start from scratch: you start with a blueprint which someone else has created, or general building instructions. You usually do not grow your own trees to get the wood, you buy wooden blocks of approximately the right size; neither do you mix paint from elemental ingredients, you assemble what others have to offer. But with those ingredients, you customize your making and end up with a very individual creation which, ideally, is exactly what you had in mind.

Containers (4): Containers with Podman

Fri, 21 Feb 2025 00:00:00 +0000

In this cluster of tutorials, you might have gotten a general overview on containers, and installed Docker. You can find instructions on how to run existing images, and take this further to building custom containers. And during the installation and use of Docker, you might have been annoyed by the mandatory administrator mode, or quirks of the Desktop App. Or you might value fully free and open source software, like I do.

Luckily, Docker is not a monolith. There are alternative approaches to containerization which mitigate some of the Docker limitations and disadvantages. In this tutorial, I will present Podman, a Docker alternative which I personally use the most (besides occasionally turning to “buildah”).