Reproducible computational environments using containers

This session aims to introduce the use of Docker containers with the goal of using them to effect reproducible computational environments. Such environments are useful for ensuring reproducible research outputs, for example.

Prerequisites

• You should have basic familiarity with using a command shell, and the lesson text will at times request that you “open a shell window”, with an assumption that you know what this means.
  • Under Linux or macOS it is assumed that you will access a bash shell (usually the default), using your Terminal application.
  • Under Windows, Powershell and Git Bash should allow you to use the Unix instructions. We will also try to give command variants for Windows cmd.exe.
• As an item of setup, it is assumed that you have a directory named container-playground that you are able to cd to using your command shell, and are also able to find using your computer’s graphical file browser (e.g., Finder on macOS or Windows Explorer). A simple way to achieve this is to create your container-playground directory within your computer’s Desktop folder. (See the Software Carpentry Shell lesson for more details.)
• The lessons will sometimes request that you use a text editor to create or edit files in particular directories. It is assumed that you either have an editor that you know how to use that runs within the working directory of your shell window (e.g. nano), or that if you use a graphical editor, that you can use it to read and write files into the working directory of your shell.