Windows WSL2 Setup

4a. Enable WSL2 on Windows 11

What is WSL2? Think of it as a lightweight Linux computer running invisibly inside Windows. GNPS Local’s analysis tools are Linux programs, so they need this Linux layer to run. You do not need to understand Linux to use it — you just need it running in the background.

Step 1: Open the Start menu, search for PowerShell, right-click it, and select “Run as administrator”.

Step 2: Copy and paste this command, then press Enter:

wsl --install

What you should see:

Installing: Virtual Machine Platform
Virtual Machine Platform has been installed.
Installing: Windows Subsystem for Linux
Windows Subsystem for Linux has been installed.
Installing: Ubuntu
Ubuntu has been installed.
The requested operation is successful.

Step 3: Restart your computer when prompted. This is required.

If you see an error like “WSL 2 requires an update to its kernel component”, run this additional command after the restart:
wsl --update

If you see “Virtualization is not enabled”, your computer’s BIOS needs a small change — see Troubleshooting.

4b. Install Ubuntu 24.04

After your restart, Ubuntu may open automatically and ask you to set up a username and password. If it does not open automatically:

Open the Start menu and search for Ubuntu.
Click Ubuntu (or Ubuntu 24.04) to open the Linux terminal.

Set up your Linux username and password:

Enter new UNIX username: yourusername
New password: (type a password — it won't show as you type, that's normal)
Retype new password:
passwd: password updated successfully

Remember this password — you will need it occasionally for system commands.

Verify WSL2 is running correctly. In PowerShell (not Ubuntu), run:

wsl --list --verbose

You should see output like:

  NAME            STATE           VERSION
* Ubuntu-24.04    Running         2

The VERSION 2 confirms WSL2 is active. You are ready to proceed.

4c. Install System Dependencies (Windows WSL2)

Before setting up your Python environment, you must ensure your Ubuntu system has the basic tools needed to run C++ analysis modules.

In your Ubuntu terminal, copy and paste this single line:

sudo apt update && sudo apt install -y build-essential libgomp1

Why is this needed? build-essential installs the C++ compiler (g++) and libgomp1 provides the library for parallel processing. GNPS Local uses these to run high-performance calculations on your data. You will be asked for your Linux password to run this.

4d. Install Conda (Miniconda) — Windows WSL2

Conda is a tool that manages Python packages — think of it as an app store for scientific Python software that keeps everything neatly organized so different tools don’t conflict with each other.

Open your Ubuntu terminal and run these commands one at a time:

Download the installer:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh

Run the installer:

bash ~/miniconda.sh

Press Enter to scroll through the license agreement.
Type yes to accept the license.
Press Enter to accept the default install location (/home/yourusername/miniconda3).
Type yes when asked to initialize conda.

Apply the changes:

source ~/.bashrc

Verify it worked:

conda --version

You should see something like conda 24.x.x. If you see “command not found”, close and reopen the Ubuntu terminal and try again.