Module 8: GitHub for Bioinformatics

This module introduces Git and GitHub for life scientists and bioinformatics trainees. Version control is a core skill in modern research computing — it lets you track changes to your scripts and data, collaborate with colleagues, and share your work with the world. By the end of this module you will have a GitHub account, a repository containing real files, and the confidence to use Git in your daily workflow.

“GitHub is where science meets code. It keeps your work safe, documented, and reproducible — and it signals to collaborators and employers that you work with professional tools.”

Learning objectives

By the end of this module, you will be able to:

• Create and configure a GitHub account
• Install and configure Git on your local machine (including WSL)
• Understand the Git workflow: stage, commit, push, pull
• Create and manage repositories on GitHub
• Track changes to bioinformatics scripts and documents over time
• Use branches to develop new features without breaking working code
• Collaborate using forks, pull requests, and issues

Lessons

• Lesson 1: Account setup and Git configuration
  • Creating a GitHub account, installing Git, and setting your identity
• Lesson 2: Your first repository
  • git init, git add, git commit, and .gitignore
• Lesson 3: Pushing to GitHub
  • Connecting a local repository to GitHub with git remote, git push, and git pull
• Lesson 4: Branches and history
  • Creating branches, switching between them, merging, and reading commit history
• Lesson 5: Collaboration and pull requests
  • Forking repositories, opening pull requests, and working with issues

Prerequisites

Before starting this module, you should be comfortable with:

• Basic Linux navigation (cd, ls, pwd) from Module 1
• Running commands from the terminal

No prior Git or GitHub experience is required.

Note: Examples in this module use small plain-text files so every command can be run immediately without large datasets.