Windows Subsystem for Linux (WSL)

1. Search for Windows Powershell 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 Powershell and then press Enter:

   Enable-WindowsOptionalFeature -Online -FeatureName Microsoft-Windows-Subsystem-Linux
   

3. Press Enter again when prompted to reboot your computer.

4. Once your computer has rebooted, open the Microsoft Store and search for “Ubuntu.” Install the program labelled “Ubuntu 18.04” (not “Ubuntu 16.04” or “Ubuntu”) by clicking the tile, pressing Get, and then Install.

5. Search for and open Ubuntu from your applications. There will be a slight delay (of a few minutes) while it finishes installing.

6. You will be prompted to Enter new UNIX username. You can use any combination of alphanumeric characters here 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 find yourself using it frequently.)

7. Right click on the top bar of the Ubuntu application and select “Properties”. Under the “Options” tab, under the “Edit Options” heading, make sure the box reading “Use Ctrl+Shift+C/V as Copy/Paste” is checked. Under the “Terminal” tab, under the “Cursor Shape” heading, make sure the box reading “Vertical Bar” is checked. Press “Okay” to save these settings and then exit the application.

(The above step-by-step WSL instructions are distilled from here and here. If you have questions during the installation procedure those resources may have answers!)

From this point on whenever the instructions specify to “open a terminal” please assume you are supposed to open the Ubuntu application.

Bash shell

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

Git

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

VSCode

1. Go to https://code.visualstudio.com/ and click the download button, then run the .exe file.
2. Leave all the defaults during the installation with the following exception:
   • Please make sure the box labelled “Register Code as an editor for supported file types” is selected

VSCode extensions

1. Open the Ubuntu application.
2. Type code . into the terminal and press Enter. You should see a message reading “Installing VS Code Server” and then a new windows will open up.
3. Press Ctrl+Shift+P in the new window that opens and type “Extensions: Install extensions” into the search bar that appears at the top of the screen. Select the appropriate entry from the dropdown menu that appears (there should be four entries; simply select the one that reads “Extensions: Install extensions”).
4. A new panel should appear on the left-hand side of the screen with a search bar. Search for each of the following extensions and press Install for the first entry that appears. (The author listed for all of these extensions should be “Microsoft”.)
   • Python (n.b., you will need to reload VSCode after installing this)
   • Docker
   • Remote - WSL

Python

1. Open a new terminal and type the following lines (separately) into the terminal, pressing 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. Exit the terminal once the installation has finished.

5. Re-open the Ubuntu application. 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 typing conda init, closing your terminal, and repeating this step. If your issue is still not resolved skip the following step and contact an instructor on the #help-installation channel on the BHS Slack.

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:

conda config --append channels conda-forge
conda config --set channel_priority strict
conda install -y flake8 ipython jupyter jupyterlab matplotlib nibabel nilearn numpy pandas scipy seaborn

Docker

Unfortunately, Docker for Windows is a bit of a mess. The recommended version of Docker to install varies dramatically depending not only on which version of Windows you have installed (e.g., Windows 10 Home versus Professional/Enterprise/Education), but also which build of Windows you have. As such, developing a comprehensive set of instructions for installing Docker is rather difficult.

For this course, you will need to install either Docker Toolbox for Windows or Docker for Windows Desktop. Which you install will depend on your OS. PLEASE NOTE that installing Docker for Windows Desktop will disable VirtualBox on your computer. If you actively use VirtualBox we recommend you install Docker Toolbox.

(Note: the below instructions assume you are installing Docker Toolbox. Because there are fewer requirements for Docker Toolbox, it is likely that you will be able to install this more easily.)

1. Download the latest Docker Toolbox installer (note: that link will automatically download the file)

2. Run the downloaded .exe file and leave all the defaults during the installation procedure. Click Yeson the prompt that appears asking if the application can make changes to your computer.

3. Search for and open the newly-installed “Docker Quickstart” application. Again, click Yeson the prompt that appears asking if the application can make changes to your computer. The application will do a number of things to finish installing and setting up Docker.

4. Once you see a $ prompt type docker run hello-world. A brief introductory message should be printed to the screen.

5. Close the “Docker Quickstart” application and open a terminal (i.e., the Ubuntu application).

6. Copy-paste the following commands. You will be prompted to enter your password once.

   # Update the apt package list.
   sudo apt-get update -y
   # Install Docker's package dependencies.
   sudo apt-get install -y \
       apt-transport-https \
       ca-certificates \
       curl \
       software-properties-common
   # Download and add Docker's official public PGP key.
   curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
   # Verify the fingerprint.
   sudo apt-key fingerprint 0EBFCD88
   # Add the `stable` channel's Docker upstream repository.
   sudo add-apt-repository \
       "deb [arch=amd64] https://download.docker.com/linux/ubuntu \
       $(lsb_release -cs) \
       stable"
   # Update the apt package list (for the new apt repo).
   sudo apt-get update -y
   # Install the latest version of Docker CE.
   sudo apt-get install -y docker-ce
   # Allow your user to access the Docker CLI without needing root access.
   sudo usermod -aG docker $USER
   

7. Close and re-open the terminal.

8. Type pip install docker-compose.

9. Type powershell.exe "docker-machine config". You should get output similar to the following:

   --tlsverify
   --tlscacert="C:\\Users\\<YOUR_USERNAME>\\.docker\\machine\\machines\\default\\ca.pem"
   --tlscert="C:\\Users\\<YOUR_USERNAME>\\.docker\\machine\\machines\\default\\cert.pem"
   --tlskey="C:\\Users\\<YOUR_USERNAME>\\.docker\\machine\\machines\\default\\key.pem"
   -H=tcp://xxx.xxx.xx.xxx:xxxx
   

   where <YOUR_USERNAME> will have an actual value (likely your Windows username), and tcp=xxx.xxx.xx.xxx:xxx will be a series of numbers. If you don't get this output then something has gone wrong. Please make sure you were able to run the docker run hello-world command, above. If you were and you still don't receive this output, please contact one of the instructors on the #help-installation channel on the BHS Slack.

10. You will use the the outputs of the above command to modify the commands below before running them in the terminal. First, take the numbers printed in place of the xs on the output of the line -H=tcp://xxx.xxx.xx.xxx:xxxx from above and replace the placeholder xxx.xxx.xx.xxx:xxxx on the first command below (export DOCKER_HOST). Second, take whatever value is printed in place of <YOUR_USERNAME> above and replace the <YOUR_USERNAME> placeholder on the second command below (export DOCKER_CERT_PATH). Once you have updated the commands appropriately, copy and paste them into the terminal:

    echo "export DOCKER_HOST=tcp://xxx.xxx.xx.xxx:xxxx" >> $HOME/.bashrc
    echo "export DOCKER_CERT_PATH=/mnt/c/Users/<YOUR_USERNAME>/.docker/machine/certs" >> $HOME/.bashrc
    echo "export DOCKER_TLS_VERIFY=1" >> $HOME/.bashrc
    

11. Close and re-open a terminal (i.e., the Ubuntu application). Type docker run hello-world. The same brief introductory message you saw before should be printed to the screen.

Note: If you restart your computer (or somehow otherwise shut down the Docker VM) you will need to re-open the “Docker Quickstart” application and wait until you see the $ prompt again before your docker commands will work again! If you are having problems running docker commands in the terminal, try re-opening the “Docker Quickstart” application.

(The above step-by-step instructions are distilled from here and here. If you have questions during the installation procedure please check those links for potential answers!)