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Containerized Bioinformatics


Containerisation is a method of bundling an application or pipeline with all its dependencies, from language runtimes like Python and R to the operating system itself. This technology has already revolutionised web development by providing a simple way to run web applications a in precisely controlled environment, regardless of which computer system they are running on.

This workshop will explain how these advantages can be easily applied to bioinformatics analysis, to ensure 100% reproducibility of your work, along with easy distribution of your pipelines to other users without the need for complex installation.

Learning Objectives

At the end of the course, you will be able to:

  • understand what containerisation is, and why you might use it in bioinformatics
  • be familiar with some common containerisation tools are, and when to use each of them
  • find and run containers built by other people
  • run containers on HPC systems (like Melbourne Bioinformatics)
  • build your own application into a container (containerisation)
  • use containers as elements of a bioinformatics pipeline, and
  • distribute your container online.


This workshop is aimed at anyone with basic Unix command-line experience.

Attendees are required to bring their own laptop computers.

Windows users should have PuTTY installed


Workshop Slides (use the arrow keys to navigate)