The Shell

Imagine trying to write an essay by selecting words from a drop-down menu. You could eventually construct sentences, but you would be limited to the words the menu designer chose for you. This is what it is like to use a GUI: the point-and-click environment you use daily. It is intuitive, but it restricts you to pre-defined actions.

As a computational biologist, you need precision and power. You need to speak to the computer directly, without a menu getting in the way. You need the Command Line Interface (CLI). In the CLI, you type text commands, and the computer obeys. It is the difference between pointing at a picture of a meal and telling the chef exactly how you want your steak cooked.

The “black box” you type into is powered by two distinct components working in tandem. It is vital to distinguish between them:

1. The Kernel: This is the core of the operating system. It controls the hardware—the CPU, memory, and hard drive. It is the “chef” in the kitchen doing the actual work.
2. The Shell: This is the program that listens to you. It takes your text command, interprets it, and tells the kernel what to do. It is the “waiter” taking your order.

The Shell operates in a continuous cycle known as a REPL (Read-Evaluate-Print Loop).

1. Read: The Shell waits for you to type a command and press Enter.
2. Evaluate: It figures out what program you want to run.
3. Print: It runs the program and displays the result on your screen.
4. Loop: It displays a prompt (usually a $) and waits for your next command.

Newcomers often confuse the Terminal with the Shell. The Terminal is the window on your screen. It accepts keyboard input and displays text. It is just a wrapper (like a television set). The Shell is the program running inside that window, processing your commands (like the broadcast showing on the TV).

Course Standards and Setup

Biology software lives on Linux. To ensure compatibility, we enforce a strict environment standard for this course.

For Windows Users

You must install the Windows Subsystem for Linux (WSL). This is not a simulator; it runs a genuine Linux kernel inside Windows.

Microsoft provides some helpful installation instructions. You should be able to open up PowerShell and run the following command to install WSL (while inside PowerShell).

wsl --install

You will then have to set up a new Linux username and password. From this point forward, all commands should be executed in your WSL.

Once you are logged in, you can update your WSL with the following bash command.

sudo apt update && sudo apt upgrade

Install the following applications in WSL to make your class experience smoother.

sudo apt-get install ssh git helix nano vim wget curl build-essential htop python3 python3-pip

Then you should install pixi using the following command.

curl -fsSL https://pixi.sh/install.sh | sh

You can still use Visual Studio Code with WSL; see here for more information.

For macOS Users

macOS is built on Unix, the cousin of Linux. You can use the default Terminal.app found in your Applications folder.

For Linux Users

You are already home. No preparation is required.

You will encounter different shells, most commonly Bash (Bourne Again Shell) and Zsh (Z Shell). For this course, they are effectively identical. If you are a beginner, stick to the default shell provided by your operating system (Bash for WSL, Zsh for modern macOS).

Learning Resources

We do not use a static textbook for this section. The Shell is a tool best learned by doing.