Lesson 1 — Account Setup and Git Configuration

Learning Objectives

Create a free GitHub account and understand what GitHub is.
Distinguish between Git (the tool) and GitHub (the platform).
Install Git on Linux, macOS, or WSL.
Configure Git with your name, email, and preferred editor.
Generate an SSH key and add it to GitHub for passwordless authentication.
Verify your setup end-to-end before writing a single line of code.

Conceptual Overview

Git vs GitHub

Git and GitHub are often mentioned together but they are different things:

Git is a version control system. It runs entirely on your local machine and tracks changes to files over time. Think of it as a detailed logbook for your code.
GitHub is a cloud platform that hosts Git repositories. It adds a web interface, collaboration features, issue tracking, and a place to back up your work.

You can use Git without GitHub, but GitHub without Git makes no sense. This module teaches both together because that is how they are used in practice.

Why version control matters in bioinformatics

Bioinformatics workflows consist of scripts, configuration files, and notes. Without version control:

You cannot easily tell which version of a script produced a particular result.
Sharing a pipeline with a collaborator involves emailing files or copying folders with names like analysis_v3_FINAL_revised2.sh.
Mistakes are hard to undo.

With Git, every change is recorded with a message, a timestamp, and the author’s name. You can always return to any previous state.

WSL note

If you are on Windows and running commands inside WSL, install Git inside WSL (not on Windows). The two environments share files but have separate software installations. Run all Git commands from inside the WSL terminal.

Worked Examples

1) Create a GitHub account

Open a browser and go to https://github.com. Click Sign up and follow the steps.

Tips:

Use an email address you check regularly — GitHub sends notifications there.
Choose a username that is professional. Many employers look at GitHub profiles.
The free plan is sufficient for everything in this module.

After signing up, verify your email address when GitHub sends the confirmation message.

2) Check whether Git is already installed

git --version

Expected output (version numbers will vary):

git version 2.43.0

If you see command not found, proceed to Example 3. If you see a version number, skip to Example 4.

3) Install Git

On Ubuntu / Debian / WSL (Ubuntu):

sudo apt update && sudo apt install git -y

Expected output (last few lines):

Setting up git (1:2.43.0-1ubuntu7) ...
Processing triggers for man-db ...

On macOS (using Homebrew):

brew install git

On macOS (without Homebrew): Running git --version on macOS will prompt you to install the Xcode Command Line Tools if Git is not present. Follow the on-screen prompt.

After installation, confirm it worked:

git --version

Output:

git version 2.43.0

4) Configure your identity

Git records your name and email with every commit. Set them once and they apply to all repositories on your machine.

git config --global user.name "Your Name"
git config --global user.email "you@example.com"

No output is expected when these commands succeed.

Replace "Your Name" with your real name and "you@example.com" with the email you used to sign up on GitHub. These values will appear in your commit history and on GitHub.

5) Set your default editor

When Git opens a text editor (for example, to write a commit message), it uses the editor stored in core.editor. The default is vi, which can be confusing for beginners.

Set it to nano, which is simpler:

git config --global core.editor "nano"

Or, if you prefer Visual Studio Code and it is installed:

git config --global core.editor "code --wait"

No output is expected when these commands succeed.

6) Set the default branch name to `main`

Older versions of Git default to naming the first branch master. GitHub now uses main. Make them agree:

git config --global init.defaultBranch main

No output is expected when this command succeeds.

7) Review your configuration

git config --list prints every setting Git knows about.

git config --list

Output (yours will differ slightly):

user.name=Your Name
user.email=you@example.com
core.editor=nano
init.defaultbranch=main

8) Generate an SSH key

An SSH key lets you push to GitHub without typing your password every time. It works as a pair: a private key that stays on your machine, and a public key that you give to GitHub.

Check whether you already have a key:

ls ~/.ssh

If you see files named id_ed25519 and id_ed25519.pub, you already have a key — skip to Example 9.

Generate a new key (replace the email with yours):

ssh-keygen -t ed25519 -C "you@example.com"

You will be prompted three times:

Enter file in which to save the key (/home/youruser/.ssh/id_ed25519):

Press Enter to accept the default path.

Enter passphrase (empty for no passphrase):

Press Enter to leave it empty for now (acceptable for a learning setup).

Enter same passphrase again:

Press Enter again.

Final output:

Your identification has been saved in /home/youruser/.ssh/id_ed25519
Your public key has been saved in /home/youruser/.ssh/id_ed25519.pub
The key fingerprint is:
SHA256:xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx you@example.com
The key's randomart image is:
+--[ED25519 256]--+
...
+----[SHA256]-----+

9) Copy your public key

Print the public key so you can paste it into GitHub:

cat ~/.ssh/id_ed25519.pub

Output (your key will be different):

ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIAbcDeFgHiJkLmNoPqRsTuVwXyZ0123456789abcdef you@example.com

Select the entire output line (starting with ssh-ed25519) and copy it to your clipboard.

10) Add the public key to GitHub

Go to https://github.com/settings/keys in your browser.
Click New SSH key.
In the Title field, enter a name for this machine (e.g. WSL Laptop).
In the Key field, paste the line you copied in Example 9.
Click Add SSH key.

11) Test the SSH connection

ssh -T git@github.com

First-time output (type yes and press Enter when asked):

The authenticity of host 'github.com (140.82.121.3)' can't be established.
ED25519 key fingerprint is SHA256:+DiY3wvvV6TuJJhbpZisF/zLDA0zPMSvHdkr4UvCOqU.
Are you sure you want to continue connecting (yes/no/[fingerprint])? yes

After you type yes:

Warning: Permanently added 'github.com' (ED25519) to the list of known hosts.
Hi YourUsername! You've successfully authenticated, but GitHub does not provide shell access.

If you see your username in that message, authentication is working correctly.

Exercises

Run git --version. What version is installed on your machine?
Run git config --list. Confirm that user.name, user.email, and init.defaultbranch are all set correctly.
Run cat ~/.ssh/id_ed25519.pub. Does the output start with ssh-ed25519? If the file does not exist, generate a key using Example 8.
Run ssh -T git@github.com. Do you see your GitHub username in the response?
Challenge: Go to https://github.com/settings/profile and add a short bio and your institution. This makes your profile more useful to collaborators.

Solutions

Solution 1

git --version

Output (version will vary):

git version 2.43.0

Solution 2

git config --list

Look for these three lines in the output:

user.name=Your Name
user.email=you@example.com
init.defaultbranch=main

Solution 3

cat ~/.ssh/id_ed25519.pub

The line should start with ssh-ed25519. If the file is missing, run:

ssh-keygen -t ed25519 -C "you@example.com"

Solution 4

ssh -T git@github.com

Expected output:

Hi YourUsername! You've successfully authenticated, but GitHub does not provide shell access.

Solution 5

Navigate to https://github.com/settings/profile, fill in the Bio and Company fields, and click Update profile.