Software

All software required for courses is open source and free unless otherwise noted. If you have any questions or problems regarding software installation, please contact your instructor.

Git and GitHub

Git is version control software, which helps you keep track of changes made to files. GitHub is a repository for data and code tracked with Git, and is a mechanism for publishing and collaborating on project development.

GitHub Desktop App for Windows, macOS

Command line tools for Windows (only for optional third week)

If you would like to work with Git on the command line in the third week of class on a Windows laptop, also install Git for Windows. Please note that this also installs Git Gui, which we will not use.

Command line tools for macOS (only for optional third week)

If you would like to work with Git on the command line in the third week of class on a Mac laptop, you will also need to install command line Git tools by clicking on “GitHub Desktop” in the top menu of the app, then selecting “Install Command Line Tool.” You will then be able to access the software through Terminal, which you can locate by clicking on your Desktop, selecting “Go” in the menu at the top, and clicking on “Utilities.”

Python

We will be using Python version 3 (and above) for our courses, as well as the following packages: pandas, jupyter notebook, numpy, matplotlib, and plotnine. We recommend installing Python using Anaconda, which includes most of the packages listed above:

Following installation, open the following command line software based on your operating system to install the final package:

R and RStudio

R and RStudio are separate downloads. R is the “engine”, while RStudio is an integrated desktop environment (IDE) that makes using R much more pleasant. R must be installed before RStudio. Follow the instructions below for your operating system to install them. If you are working on a computer owned by Fred Hutch, it may also be possible to install these programs through the self-service app.

Windows

macOS