Set up WSL2 and Ubuntu.

Before you start

Many bioinformatics tools run in Linux. Windows Subsystem for Linux (WSL) lets you use a Linux environment on the same PC as your familiar Windows desktop. Ubuntu is the Linux distribution used in this lesson.

• Use Windows 11, or Windows 10 version 2004, build 19041 or later.
• Have an internet connection and administrator access for installation.
• Allow about 10 minutes for the exercise, with extra time for downloads and a restart.

These installation requirements and commands follow Microsoft’s WSL installation guide.

Step 01 · Windows PowerShell

Install WSL and Ubuntu

Search for PowerShell in Windows, choose Run as administrator, and enter:

wsl --install

Restart Windows when prompted. Then find Ubuntu in the Start menu and open it. On first launch, choose your Linux username and password.

Already have WSL and Ubuntu installed? Continue with the checks below. First-launch account behaviour is described in Microsoft’s environment setup guide.

Step 02 · Check, then explore

Check your environment

Back in Windows PowerShell, run:

wsl --list --verbose

Find Ubuntu and check that its VERSION column is 2. Its state may be Running or Stopped. If you see version 1, refer to the version-conversion section of Microsoft’s installation guide before continuing.

Now open Ubuntu and try these commands, one line at a time:

whoami
pwd
ls

whoami

Show the Linux username you are using.

pwd

Show your current directory.

ls

List the files and folders there. An empty folder can produce no output.

Step 03 · Ubuntu terminal

Create your first workspace

Run these commands in Ubuntu, one line at a time. The ~ symbol refers to your Linux home directory.

mkdir -p ~/bioinformatics_training
cd ~/bioinformatics_training
mkdir -p data results
printf "Bioinformatics starts here\n" > README.txt
ls -lh

The final command should list two folders and one text file. File sizes, dates, and your username will differ.

bioinformatics_training/
├── data/
├── results/
└── README.txt

data/

Keep input files here.

results/

Keep the output of your exercises here.

README.txt

Keep a short note about the project.

A clear folder structure makes it easier to understand your work when you return to it. We will build on this workspace in later lessons.

Step 04 · Five-minute challenge

Make one small thing yourself.

Inside bioinformatics_training, create a folder called lesson01 and a file inside it called notes.txt. Put one sentence about what you learned in the file.

Use mkdir, cd, and printf or echo. Check your result with ls.

bioinformatics_training/
└── lesson01/
    └── notes.txt

Once you have tried it, share what worked or the question that stopped you in the original lesson discussion.

If you get stuck