3-containers.qmd

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title: "3. Containerizing R and R Packages for Ultimate Reproducibility"
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![](media/images/blocks-containers.png)

This section consists of four parts. Part *a* is a reference material, parts *b*, *c*, and *d* are tutorials, but you probably will not have time to go through both in class, so choose one of them to do in class and do the rest at home.

a. The overview of how containers work: [Get Familiar with `Docker` and `Binder`](3a-how-docker-and-binder-work.qmd). This is more of a reference material that explains some technicalities of `Docker` (one of the popular containerization software) and `Binder` (an online service that allows you to run a container with `R` and `RStudio` in the cloud with just a web browser).

b. A tutorial for [making your own git repository reproducible in `Binder`](3b-reproducible-github-repo-in-binder.qmd). It focuses on how to setup your `git` repository in such a way, so that anyone can run it in the cloud using `Binder` with just a web browser. The primary use case for this is publishing a reproducible repository for a research project, primarily with code that reproduces figures from raw data or pre-calculated and cached modelling results. `Binder` is limited in memory and compute power, so it will not handle long running resource intensive computation.

c. A tutorial for [building your own `Docker` container image with `R` and R packages pre-installed and run it locally](3c-build-docker-container-image.qmd). It covers the process of customizing the `Dockerfile` and building the container image locally on your computer. You would normally use such container image for everyday work locally on in the academic High Performance Computing (HPC) cluster or on your own personal computer. **Note: due to recent changes to [`Play with Docker`](https://www.docker.com/play-with-docker/){target="_blank"}, you will not be able to build large container images, therefore if you do not have `Docker` installed on your computer, you will only be able to use `Play with Docker` to build a slighly simpler container image that is unrelated to the project we were working on in other parts of the tutorial.**

d. A tutorial for those who want to try `Docker`, but cannot install it. [`Play with Docker`](https://www.docker.com/play-with-docker/){target="_blank"} allows a similar experience in a web browser. [Try `Docker` in a web browser via `Play with Docker`](3d-play-with-docker.qmd).