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Linux Setup
Instructions for setting up on Linux

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:

  1. 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 yum install git (Fedora) inside the terminal. If you are prompted to install it follow the instructions on-screen to do so.

VSCode

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

VSCode extensions

  1. Open the Visual Studio Code application.
  2. 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").
  3. 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)
    • Live Share (n.b., you may need to press "Ctrl/Cmd+Shift+P" and type "install extensions" again after installing this)
    • Live Share Extension Pack
    • Docker

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 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 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 create -n qlsc612 -y python=3.9 flake8 ipython jupyter jupyterlab matplotlib nibabel nilearn numpy pandas scipy seaborn bokeh
conda activate qlsc612

Docker

  1. You will be following different instructions depending on your distro (Ubuntu, Debian, Fedora, CentOS). Make sure to follow the “Install using the repository” method!
  2. 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.
  3. Open a new terminal and type docker run hello-world. A brief introductory message should be printed to the screen.

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