Version Control with Git

“branch early, and branch often”

You should version control your scripts with Git.

Learning resources: https://swcarpentry.github.io/git-novice/01-basics.html

https://happygitwithr.com/

I recommend the Using Git and GitHub with RStudio Cheatsheet for additional helpful commands.

UK Biobank Audit tool

https://github.com/UK-Biobank/UKB-Git-Audit-Tool

scan to prevent sensitive data (PHI) from being committed to Git repositories.

GitHooks to check for specific items of data and ensure they are not committed

No data. No credentials. No tokens. No Jupyter notebooks that may inadvertently contain sensitive data in the output cells. Use .gitignore to exclude data folders.

Important

As long as you have your raw data backed up and your scripts version controlled, you can reproduce your results!

GitHub SSH Setup (macOS)

Set up SSH authentication for GitHub so you can push/pull to both personal and lab repos without credential issues.

1. Set Your Git Identity

git config --global user.name "Your Name"
git config --global user.email "your-email@vumc.org"

2. Generate a Key

ssh-keygen -t ed25519 -C "your-email@vumc.org" -f ~/.ssh/id_github

Set a passphrase when prompted (use 4+ random words like blue-microscope-river-42).

3. Add to macOS Keychain

ssh-add --apple-use-keychain ~/.ssh/id_github

4. Configure SSH

Create ~/.ssh/config:

Host github.com
    IdentityFile ~/.ssh/id_github
    UseKeychain yes
    AddKeysToAgent yes

5. Add Key to GitHub

pbcopy < ~/.ssh/id_github.pub

Go to GitHub.com → Settings → SSH and GPG Keys → New SSH Key, paste, and save.

6. Test

ssh -T git@github.com
# Hi <username>! You've successfully authenticated...

7. Clone and Remote URLs

Always use the SSH format with a colon (not a slash) after github.com:

# Cloning
git clone git@github.com:krantzlab/repo-name.git

# Switching an existing repo from HTTPS to SSH
git remote set-url origin git@github.com:krantzlab/repo-name.git

Troubleshooting

Problem	Fix
`Permission denied (publickey)`	Run `ssh-add -l` to check if key is loaded. Re-add with `ssh-add --apple-use-keychain ~/.ssh/id_github`
`does not appear to be a git repository`	Check your remote URL — make sure it uses `:` not `/` after `github.com`
Passphrase prompt every time	Verify `UseKeychain yes` is in `~/.ssh/config`

Setting Up SSH for GitHub on Terra

Reference for setting up SSH for GitHub on Terra:

https://github.com/DataBiosphere/terra-examples/blob/main/best_practices/source_control/terra_source_control_cheatsheet.md

You need to do this one time for each new workspace you create on Terra (You need to run source ~/.bashrc every time you resume your workspace to start ssh and the path for your public key)

These code blocks are meant to be copied and pasted to run in the command line.

Step 1

git config --global user.name "<username>"
git config --global user.email "<email>"

Step 2

# set your github user.name
git config --global user.name "<username>"

# set your github user.email
git config --global user.email "<email>"

# start the ssh agent
ssh-agent -s

# make a directory to later save your ssh key (public and private key)
mkdir -p ~/.ssh

# create your ssh key pair
ssh-keygen -t ed25519 -f ~/.ssh/id_ed25519 -C "me@institution.org"

# you don't have to specify a key password, just leave empty and press enter

# print your ssh public key to your terminal to copy and paste when adding a new new SSH key at https://github.com/settings/keys
cat ~/.ssh/id_ed25519.pub

Step 4

Add your public key to your github SSH keys. This has to be done on github, https://github.com/settings/keys

Step 5

# add start ssh-agent to your .bashrc profile
echo 'eval "$(ssh-agent -s)"' >> ~/.bashrc

# add the path to your SSH key
echo 'SSH_KEY=~/.ssh/id_ed25519' >> ~/.bashrc

# add your ssh key using it path
echo 'ssh-add "$SSH_KEY"' >> ~/.bashrc

# run your updated .bashrc profile
source ~/.bashrc

Git Clone

git clone git@github.com:<username>/<reponame>.git

Create a New Repository on GitHub

Go to GitHub to create your new repository, then initialize your repository from the command line.

cd </path/to/your-r-project-folder>
echo "# your-r-project-folder" >> README.md
git init
git add README.md
git commit -m "first commit"
git branch -M main
git remote add origin https://github.com/<user.name>/<your-repository>.git
git push -u origin main

Add, Commit, and Push Files to Remote Repository

git add <file-name>
git commit -m "description"
git push