WSL2 (Windows Subsystem for Linux version 2)

WSL (Windows Subsystem for Linux) allows you to use Linux on top of Windows natively. WSL2 is the latest version of WSL and is more stable with improved performance and compatibility. If you already have WSL(1), it is easy to convert to WSL2 (see Instructions to convert WSL(1) to WSL2). If your Windows 10 is version 1909 or older, see the “Install WSL2 on Windows 10 (older versions)” section on this page.

Install WSL2 on Windows 10 or 11

  1. Open Start (Win key) and search for Command Prompt (type directly) in your applications, right-click and select Run as administrator. Select Yes on the prompt that appears asking if you want to allow the app to make changes to your device.

  2. Type the following into the Command Prompt, then press Enter:

    wsl --install
  3. Restart your computer to finish the WSL installation and continue with the Linux distro setup.
  4. Open Start (Win key) and search for Command Prompt in your applications, right-click and select Run as administrator. Select Yes on the prompt that appears asking if you want to allow the app to make changes to your device.
  5. At this point, if you are on a newer version of Windows 10 or Windows 11, the command from Step 2 should have installed, in addition to WSL, the latest LTS version of Ubuntu (24.04 LTS at time of writing) as the default distribution. If this is the case, an Ubuntu terminal will open to resume automatic setup, and afterwards will ask you set up a username and password. If this applies to you, skip to Step 9. Otherwise, continue with Step 6.

  6. In the Command Prompt, type the following command to view a list of available WSL distros you can install and press Enter:

    wsl --list --online

  7. Type the following command to install a specific distro (Ubuntu-22.04 recommended) in WSL and press Enter (it will start the distro if it has already been installed):

    wsl --install -d <DISTRO-NAME>
  8. Restart your computer, open Start (Win key) and search for Ubuntu, and click on the app called Ubuntu or Ubuntu <VERSION-NUMBER>. You should now have the WSL2 Ubuntu 22.04 terminal open. Now, you are ready to rock!
  9. You will be prompted to Enter new UNIX username (this will create a local user account for the Ubuntu WSL instance and you will be automatically logged in to your Ubuntu distro as this user). You can use any combination of alphanumeric characters for your username, but a good choice is <first_initial><last_name> (e.g., jsmith for John Smith). You will then be prompted to enter a new password (choose something easy to remember as you will use it frequently for this course).

From this point on, whenever the instructions specify to “open/type a command in a terminal”, please open/type the command in the Ubuntu application (open Start (Win key), search for Ubuntu, and click Ubuntu or Ubuntu <VERSION-NUMBER>).

Need more help?

Bash shell (in the WSL2 Ubuntu)

You already have it, now that you’ve installed the WSL2!

Git (in the WSL2 Ubuntu)

You already have it, now that you’ve installed the WSL2!

Git configuration

If you have never used Git on your computer, you may have to configure it. The following instructions assume you have already created a GitHub account.

Type the following commands in a terminal. Make sure to use the email associated with your GitHub account. The user.name can be any name you want to appear as the author of your commits, but we recommend using the name associated with your GitHub profile. 

git config --global user.name "Jane Doe"
git config --global user.email "janedoe@example.com"
git config --global core.autocrlf true

Tip: You can review your configuration at any time with: git config --list

Creating an SSH key for GitHub

When following the GitHub docs below, make sure to select the Linux instructions.

To authenticate to GitHub from the command line, you will use an SSH key pair, which is more secure than using your GitHub account password directly.

  1. In a terminal, check if you have existing SSH keys in the ~/.ssh directory. A public/private key pair typically has the filename format id_ALGORITHM and id_ALGORITHM.pub. If you have existing key files, use a custom name for your SSH key pair in step 2.
  2. Generate a new SSH key and add it to the ssh-agent.
    • Ensure to use the default file location for saving the key, unless you already have existing keys - in this case, replace just the id_ALGORITHM (e.g., id_ed25519) part of the file location with an informative keyname like id_ed25519_github
    • Choose a passphrase you can remember easily, as you will need to use it for certain Git commands
  3. Confirm your key pair was created by running the command: 
    ls -la ~/.ssh
    You should see two files with your key name, one with .pub (the public key) and one without (the private key - do not share or copy this file!).
  4. Add the SSH key to your GitHub account.
    • Be careful when copying/pasting the public key to not accidentally add spaces or newlines
    • Choose Authentication Key for the key type
  5. Locally specify the SSH key to use when connecting to GitHub, so that the right "identity" is always used for local Git operations (useful when you have multiple keys).
    1. Run the following command (replace id_ed25519 with your private key's filename if you used a custom key name): 
      printf 'Host github.com\n  User git\n  IdentityFile ~/.ssh/id_ed25519\n  IdentitiesOnly yes\n' >> ~/.ssh/config
    2. Then, check that the config was added: 
      cat ~/.ssh/config
      You should see something like: 
      Host github.com
  User git
  IdentityFile ~/.ssh/id_ed25519
  IdentitiesOnly yes

In this course, when using a Git command that prompts you for your passphrase, enter the passphrase you set for your private key in step 2.

VSCode (on your Windows)

  1. Go to this page and click the download button, then run the .exe file.
  2. Leave all the defaults during the installation with the following exception:
    • Make sure the box labeled “Register Code as an editor for supported file types” is selected

VSCode extensions

These extensions will allow you to work with WSL2 Ubuntu more seamlessly in VSCode.

  1. Open Visual Studio Code, click on the Extensions icon in the left sidebar (or press Ctrl+Shift+X), and search for and install the WSL extension (usually, VSCode can automatically detect your WSL Ubuntu installation and remind you to install related extensions).
  2. In a terminal (Ubuntu), type code . and press Enter. You should see a message reading Installing VS Code Server and then a new VSCode window (might be called Get Started - <USERNAME> [WSL: Ubuntu <VERSION-NUMBER>] Visual Studio Code) will open up. It should say WSL in the bottom left corner of the window.
  3. In the WSL VSCode window, open the Extensions panel again (or Ctrl+Shift+X). Search for each of the following extensions and click Install (or Install in WSL: Ubuntu, depending on whether you already have the extension installed locally) for the first entry that appears. If no Install button is available and the extension is not grayed out, it means it is already installed.
Required extensions

To confirm the extensions have been installed correctly, clear the Extensions search bar. You should now see an extensions category called WSL: UBUNTU - INSTALLED (you may also see one for LOCAL - INSTALLED). Verify that the extensions you have just installed exist in the list under WSL: UBUNTU - INSTALLED.

WSL2 Ubuntu terminal in VSCode

You can open the terminal in your WSL VSCode window (if you do not already have one at the bottom of the window) by navigating to View > Terminal in the top menu bar (or, Ctrl+`). This terminal in a WSL VSCode window is equivalent to the WSL2 Ubuntu terminal we get from opening the Ubuntu app itself (i.e., like we did from the Start (Win key) menu), but with the advantage of having all the graphical features of VSCode at your disposal.

Reference: https://code.visualstudio.com/docs/remote/wsl

Python (in the WSL2 Ubuntu)

We are going to install miniconda to manage the Python environment in our WSL2 Ubuntu using the VSCode terminal (alternatively, you can use the WSL Ubuntu terminal directly: open Start (Win key) and search for the Ubuntu app).

  1. Type the following lines (separately) into the terminal and press Enter after each one:

    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
  2. A license agreement will be displayed and the bottom of the terminal will read --More--. Press Enter or the space bar until you are prompted with Do you accept the license terms? [yes\|no]. Type yes and then press Enter.
  3. The installation script will inform you that it is going to install into a default directory (e.g., /home/$USER/miniconda3). Leave this default and press Enter.
  4. When you are asked “Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no],” type yes and press Enter. Close the terminal once the installation has finished.
  5. Re-open the Ubuntu terminal. Type which python into the terminal and it should return a path (e.g., /home/$USER/miniconda3/bin/python).
    • If you do not see a path like this then please try cd miniconda3/bin/ then ./conda init, close (or re-open) your terminal, and repeat this step. If your issue is still not resolved skip the following step and contact an instructor on the #help-installation channel on the Slack workspace.

  6. Type the following to remove the installation script that was downloaded:

    rm ./Miniconda3-latest-Linux-x86_64.sh

Python packages

Open a terminal and type the following commands (press Enter after each): 

conda config --append channels conda-forge
conda config --set channel_priority strict
conda create -n qlsc612 -y python=3.12 flake8 jupyterlab jupyter nilearn matplotlib seaborn bokeh statsmodels plotly wordcloud
conda activate qlsc612

This installation step (conda create) will take a couple minutes. The above commands create a new conda Python environment named qlsc612 with all the necessary packages installed for this course. The last line, conda activate qlsc612, will activate this Python environment (the default environment is base).

Now you are ready to use VSCode to edit your Python script or Jupyter Notebook in your WSL2 Ubuntu distribution.

Reminders:

Docker Desktop for Windows

You should install Docker Desktop after you have successfully installed WSL2.

  1. Go to this page and click “Docker Desktop for Windows”, then run the downloaded installer.
  2. When prompted, ensure the “Use WSL 2 instead of Hyper-V option” on the Configuration page is selected.
  3. Follow the instructions on the installation wizard to authorize the installer and proceed with the install.
  4. When the installation is successful, click “Close” to complete the installation process. (If the admin account on your computer is different to your user account, you must add the user to the docker-users group. Run Computer Management as an administrator and navigate to Local Users and Groups > Groups > docker-users. Right-click to add the user to the group. Log out and log back in for the changes to take effect.)
  5. Open Start (Win key), search for Docker Desktop in your applications, and click to run the app. Once Docker Desktop has loaded, in a WSL2 Ubuntu terminal (in VSCode or your Ubuntu app), type docker run hello-world. A brief introductory message should be printed to the screen.

Reminders:

The above step-by-step instructions are distilled from here.