Content developed by Ben Rambo-Martin and Kristine Lacek

Prerequisites

1.1 Check your Windows version

Select ⊞ Win + R, type winver, and click OK.

Requirement: Windows 10 version 2004+ (Build 19041+) or Windows 11.
Update via Start → Settings → Windows Update → Check for updates if needed.

1.2 What is WSL?

WSL (Windows Subsystem for Linux) lets you run a full Linux environment directly on Windows without a virtual machine or dual-boot setup. WSL2 is the recommended version — it uses a real Linux kernel and offers full system-call compatibility.

Key benefits:

  • Run Linux command-line tools (bash, grep, sed, awk, etc.)
  • Install and run bioinformatics software natively
  • Access the Windows filesystem from Linux and vice-versa

Install WSL2 and Ubuntu

2.1 Open PowerShell as Administrator

Right-click the Start button and select Windows PowerShell (Admin) or Terminal (Admin).

Open PowerShell as Administrator

2.2 Install WSL

Run the following command in PowerShell:

wsl --install
Tip: To paste into a terminal, use right-click instead of Ctrl+V.
If this command errors out, you may need to enable virtualization.

2.3 Restart your computer

Restart now before continuing to the next step.

2.4 Install Ubuntu 20.04

Reopen PowerShell as Administrator and run:

wsl --set-default-version 2
wsl --install -d Ubuntu-20.04
If either command errors out, see the WSL troubleshooting guide.

An Ubuntu terminal should open automatically:

Ubuntu setup prompt

User Account Setup

3.1 Create your WSL user account

When the Ubuntu terminal opens for the first time:

  1. Enter a username (exclusive to WSL) and press Enter.
  2. Enter a password and press Enter.
Important: Choose a memorable password. If you forget it, you will need to reinstall Ubuntu.

A prompt will appear similar to:

WSL command prompt

where nbx0 is replaced by your username and L349232 by your computer name.

3.2 Restart your computer

Restart one more time to finalize the setup.

Post-Install Verification

4.1 Open Ubuntu

Search for Ubuntu in the Windows taskbar and click the app icon:

Open Ubuntu from taskbar

4.2 Verify your installation

Run the following commands to confirm everything is working:

# Check Ubuntu version
lsb_release -a

# Check your username
whoami

# Check WSL version from PowerShell (open a separate PowerShell window)
# wsl --list --verbose

4.3 Verify Linux mount in File Explorer

Windows 11 (and updated Windows 10) should automatically mount Linux in File Explorer.

Linux in File Explorer

If you do not see "Linux" in File Explorer, you need to map the WSL network drive.

4.4 Understanding your file system

Inside WSL you have two main locations:

Path Description
/home/<username>/ Your Linux home directory (fast, native Linux filesystem)
/mnt/c/ Your Windows C: drive mounted inside Linux
Best practice: Store project files in your Linux home directory (~/) for best performance. Access Windows files via /mnt/c/ when needed.

4.5 Useful references