Linux Setup

Bash shell

You already have it! Depending on which version of Linux you’re running you may need to type bash inside the terminal to access it. To check whether this is necessary, follow these steps:

Open a terminal and type echo $SHELL.
- If it reads /bin/bash then you are all set!
- If not, whenever the instructions read open a terminal, please assume you are to open a terminal, type bash, and the proceed with the instructions as specified.

Git

You may already have it; try typing sudo apt-get install git (Ubuntu, Debian) or sudo dnf install git (Fedora) inside the terminal. If you are prompted to install it follow the instructions on-screen to do so.

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.

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.
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
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!).
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
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

Go to this page and click the download button for either the .deb (Ubuntu, Debian) or the .rpm (Fedora, CentOS) file.
Double-click the downloaded file to install VSCode (you may be prompted to type your administrator password during the install).

VSCode extensions

Open the Visual Studio Code application.
Open the Extension side panel by pressing Ctrl+Shift+X. In the search bar at the top of this panel search for each of the following extensions and press Install for the first entry that appears.

Required extensions

Python Extension Pack (note: you will need to reload VSCode after installing this)
Jupyter
Docker
WSL

Python

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

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
The installation script will inform you that it is going to install into a default directory (e.g., /home/$USER/miniconda3). Leave this default and press Enter.
When you are asked “Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no],” type yes and press Enter. Exit the terminal once the installation has finished.
Re-open a new terminal. Type which python into the terminal and it should return a path (e.g., /home/$USER/miniconda3/bin/python).
- If you do not see a path like this then please try 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 of the Slack workspace.
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).

Docker

You will be following different instructions depending on your distro (Ubuntu, Debian, Fedora, CentOS). Make sure to follow the “Install using the repository” method!
Once you’ve installed Docker make sure to follow the post-install instructions as well. You only need to do the “Manage Docker as a non-root user” and “Configure Docker to start on boot” steps.
Open a new terminal and type docker run hello-world. A brief introductory message should be printed to the screen.