Chapter 0: Setting Up Your Lab

The Hard Truth

Bioinformatics tools (SAMtools, BWA, etc.) are built for Linux. They do not have .exe installers. They do not run on standard Windows.

To follow this guide, you need a Terminal.

🪟 For Windows Users (Critical)

Do not use Command Prompt (cmd) or PowerShell. They are not compatible with most biological tools.

You must install WSL (Windows Subsystem for Linux). This puts a real Ubuntu Linux system inside your Windows laptop.

How to Install WSL

1. Open PowerShell as Administrator (Right-click Start Menu -> Terminal (Admin)).

2. Type this command and hit Enter:

   wsl —install

3. Restart your computer.

4. When it restarts, a window will pop up asking you to create a “UNIX Username” and “Password”.

   • Note: When typing the password, nothing will show on screen. This is normal security.

5. Congratulations. You now have a Linux terminal. Open the app called “Ubuntu” to start.

🍎 For Mac Users

You are lucky. macOS is built on UNIX, just like Linux.

1. Press Cmd + Space.
2. Type Terminal.
3. Press Enter.
   • Optional but recommended: Install iTerm2 for a better experience.

🐧 For Linux Users

You are already home.

1. Press Ctrl + Alt + T (on Ubuntu/Debian).
2. Or search for Terminal in your app menu.

Verify Your Setup

Open your new terminal (Ubuntu on Windows, Terminal on Mac) and type:

echo “Hello Bioinformatics”

If it prints Hello Bioinformatics back to you, you are ready for Chapter 1: Navigation.