This series of Docker tutorials have biochemists, biologists and non-IT scientists in mind. The general goal is to learn how to harness this quasi-Universal software to run (mostly linux-based) software onto a Mac or Windows computer, providing access to otherwise difficult to install software, or software that only runs on Linux.
There are no strong pre-requisites to follow, but a familiarity to navigate within a Terminal by command line is essential. For this purpose the Unix/Linux/bash-basics tutorials would suffice.
Useful updates:
Important note (oct 07, 2024): changes in the licensing of Docker Desktop has changed.
It is no longer recommended to UW personnel to download Docker Desktop to install Docker.
Therefore, the following alternative is now suggested: Podman which offers a system that is compatible with native Docker images and also has a Podman Desktop software that has a similar interface as Docker Desktop.
Once the software is installed (see below) commands such as docker run can be replaced with podman run.
– Download: podman.io
– Installation: podman.io/docs/installation
– Tutorials: https://docs.podman.io/en/latest/Tutorials.html
– Video tutorial: Podman Tutorial Zero to Hero | Full 1 Hour Course
More details at the top of this page: 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.
TUTORIALS –
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)
- Blog Notes: “Remove stopped containers“
- Part 2: Docker – Beginner Biologist 2: (last updated: December 10, 2019)
- Blog Notes: “Shell access to running container“
- Part 3: Docker – Beginner Biologist 3: (last updated: December 17, 2019)
- HTML,
- PDF from HTML,
- PDF (BioCstyle-no colored background)
- Slides (ioslides – see below)
- Exercise files:
- GIP.fa, GLP-1.fa, GLP-2.fa, glucagon.fa
- SRR10314868 (Click “Data Access” tab to see download link – size: 77Mb)
- Blog Notes: “Bypass Entrypoint“
- Part 4: Docker – Beginner Biologist 4: (last updated: December 19, 2019)
- HTML,
- PDF from HTML,
- PDF (BioCstyle-no colored background)
- Slides (ioslides – see below)
- Exercise files: iris-names.csv, (from: iris.data, iris.names,) rho_homo_sapiens.fa
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.
Computer
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:
www.docker.com/products/docker-desktop
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.