Windows Subsystem for Linux (WSL) installation guide

This guide will help you install WSL on Windows to run Linux-based bioinformatics tools.

Prerequisites

Windows 10 version 2004 or higher, or Windows 11
At least 20 GB free disk space

Installation steps

Method 1: Simple installation (Windows 11 or Windows 10 version 2004+)

Open PowerShell or Command Prompt as Administrator
- Right-click Start menu → “Windows Terminal (Admin)”
Run the following command:

wsl --install

Restart your computer when prompted
After restart, Ubuntu will automatically install and ask you to:
- Create a username (lowercase, no spaces)
- Create a password (you won’t see characters as you type)

Method 2: Manual installation (Older Windows versions)

Enable WSL Feature

dism.exe /online /enable-feature /featurename:Microsoft-Windows-Subsystem-Linux /all /norestart

Enable Virtual Machine Platform

dism.exe /online /enable-feature /featurename:VirtualMachinePlatform /all /norestart

Restart your computer
Download and install the WSL2 Linux kernel update
- Visit: https://aka.ms/wsl2kernel
- Download and run the installer
Set WSL2 as default

wsl --set-default-version 2

Install Ubuntu from Microsoft Store
- Open Microsoft Store
- Search for “Ubuntu 22.04 LTS”
- Click “Get” to install

Post-installation setup

1. Update Ubuntu

Before proceeding with the installation, it’s important to ensure your system packages are up to date. This step updates the package lists and upgrades all installed packages to their latest versions.

# Refresh the package index,
sudo apt update

# Perform the actual upgrade with automatic confirmation (`-y` flag).
sudo apt upgrade -y

2. Install essential tools

sudo apt install -y build-essential curl wget git vim nano unzip ca-certificates

3. Verify installation

# Check Ubuntu version
lsb_release -a

# Check available disk space
df -h

# Check WSL version
wsl --list --verbose

Accessing Windows files from WSL

Your Windows drives are mounted under /mnt/:

# Access C: drive
cd /mnt/c/

# Access D: drive
cd /mnt/d/

# Navigate to your Documents folder
cd /mnt/c/Users/YOUR_USERNAME/Documents/

Accessing WSL Files from Windows

In Windows File Explorer, type:

\\wsl$\Ubuntu\home\YOUR_USERNAME

Or access via:

File Explorer → Linux → Ubuntu

Troubleshooting

Issue: “WSL 2 requires an update to its kernel component”

Solution: Download and install the WSL2 kernel update from https://aka.ms/wsl2kernel

Issue: Installation hangs or fails

Solution:

# Reset WSL
wsl --shutdown
wsl --unregister Ubuntu-22.04
wsl --install

Issue: “This app can’t run on your PC”

Solution: Ensure virtualization is enabled in BIOS/UEFI settings

Issue: Slow performance

Solution: Ensure you’re using WSL2, not WSL1

wsl --set-version Ubuntu-22.04 2

CPG Bioinformatics Nepal Training Feb 2026