Docker container illustration

Docker – Beginner for Biologists

Useful updates:

Install Local Docker Desktop on macOS without Admin

– In tutorials below Windows users should replace command containing -v $(pwd) with the “universal” writing -v ${PWD} that is suitable for all systems.


The tutorials are presented in different formats, HTML and PDF. The HTML version shows some code with a color-coded background that does not show on the “standard” PDF. Therefore an HTML-derived PDF is also offered.

  • Part 1:  Docker – Beginner Biologist 1: (last updated: December 5, 2019)
    • HTML,
    • PDF from HTML,
    • PDF (BioCstyle-no colored background)
    • Slides  (ioslides – see below)
  • Blog Notes: “Remove stopped containers

Slides – ioslides. The following single character keyboard shortcuts enable alternate display modes:

    • 'f': enable fullscreen mode
    • 'w': toggle widescreen mode
    • 'o': enable overview mode
    • 'h' enable code highlight mode

Short Preparations:

Docker registration

To use Docker one needs to be registered (free) on their web site. It may be useful to register before class tomorrow by going to this page:

You will then have a docker username that you’ll need to run the docker program in class. If necessary we can proceed to the registration in class.


The plan is to use the classroom iMacs.

If you have a Macbook and would prefer to use that in class that should be OK provided that you can installDocker on it. Docker has hardware requirements that older computer might not meet. You would need your docker username to be able to download from:

Note: While docker does also run on Windows, there are some hurdles to run it smoothly (e.g. need to create a user group within the computer with an Admin password.) Therefore for now I will only teach in class on Macintosh systems or possibly on a Linux system. We can discuss running on Windows in or after class.