Git & GitHub Setup

Version control configuration

Modified

February 1, 2026

Git Learning Path — This is the first of 3 pages covering Git for the lab. Setup → GitHub Fundamentals → Git Practices

Beginner 10 min read Git Phase 1: Setup

Next: GitHub Fundamentals →

Version control is essential for all lab work. This guide covers installing and configuring Git and GitHub.

Install Git

Platform Method
Longleaf module load git (already available)
macOS xcode-select --install or brew install git
Linux sudo apt install git
Windows Git for Windows (includes Git Bash)

Configure Git

These settings identify your commits:

git config --global user.name "Your Name"
git config --global user.email "your.email@unc.edu"

# Recommended settings
git config --global init.defaultBranch main
git config --global pull.rebase false

Explanation:

  • user.name and user.email: Attached to every commit you make
  • init.defaultBranch main: New repos use main instead of master
  • pull.rebase false: Use merge commits when pulling (simpler for beginners)

SSH Keys for GitHub

SSH keys let you push/pull without entering your password each time.

Generate a Key

# Generate key (if you don't have one)
ssh-keygen -t ed25519 -C "your.email@unc.edu"

Press Enter to accept the default file location. You can add a passphrase for extra security.

Add Key to SSH Agent

# Start ssh-agent
eval "$(ssh-agent -s)"
ssh-add ~/.ssh/id_ed25519

Add Key to GitHub

# Copy public key
cat ~/.ssh/id_ed25519.pub

Then add to GitHub:

  1. Go to GitHub –> Settings
  2. Click SSH and GPG keys
  3. Click New SSH key
  4. Paste your public key
  5. Give it a descriptive title (e.g., “Longleaf” or “MacBook”)

Test the Connection

ssh -T git@github.com
# Should say: "Hi username! You've successfully authenticated..."

Git on Longleaf with OnDemand

If using OnDemand + RStudio for development:

Initial Setup (One Time)

  1. Launch RStudio Server via OnDemand
  2. Open Terminal tab in RStudio
  3. Configure Git (see above)
  4. Set up GitHub authentication:

Option A: HTTPS with credential caching

git config --global credential.helper 'cache --timeout=28800'
git clone https://github.com/rashidlab/your-repo.git

You’ll enter your username and personal access token once, and it caches for 8 hours.

Option B: SSH keys (more permanent)

ssh-keygen -t ed25519 -C "your_onyen@unc.edu"
cat ~/.ssh/id_ed25519.pub
# Copy this key to GitHub: Settings --> SSH Keys --> New SSH Key

Daily Workflow

  1. Launch RStudio via OnDemand

  2. Open your project (File –> Open Project)

  3. Pull latest: git pull origin main

  4. Work on code

  5. Commit and push:

    git add -A
git commit -m "feat: add new analysis function"
git push origin main

RStudio Git Integration

RStudio has built-in Git support:

  • Git tab in top-right pane shows changed files
  • Diff button shows changes
  • Commit button opens commit dialog
  • Pull/Push buttons sync with remote

To enable: Tools –> Project Options –> Git/SVN –> Select Git

Verification Checklist

After setup, verify Git and GitHub work correctly:

On Longleaf

ssh your_onyen@longleaf.unc.edu
module load git
git --version
git config --list | grep user
ssh -T git@github.com

Locally

git --version
git config --list | grep user
ssh -T git@github.com
gh --version
gh auth status

Test a Clone

# Test SSH access
git clone git@github.com:rashidlab/lab-handbook.git test-clone
rm -rf test-clone

Common Issues

Issue Solution
Permission denied (publickey) SSH key not set up; see SSH Keys for GitHub
Authentication failed Use SSH instead of HTTPS, or use a personal access token
Git not found Load module on Longleaf (module load git) or install locally

For more detailed troubleshooting, see Troubleshooting.

Next Steps

Next: GitHub Fundamentals | First Project