1. Introduction to The Shell

What is “the shell”?

  • Most of us interact with computers day-to-day via graphical user interfaces
    • Windows with file contents we navigate with a mouse.
  • To automate common research tasks, interact with computers through a shell (sometimes called the command line).
    • In this class and in almost all research/industry environments, we use a Unix (Linux/Mac) shell (Windows has a shell too, but it’s not used much).

  • The shell allows you to interact with your computer via text commands.

  • You can also write scripts that automate those interactions.

Accessing the shell

  • Mac users: access the shell through the Terminal app.

  • Windows users: have to install third-party software to use the “right” shell
    • open windows powershell
    • Windows 10+ users: To run a Linux shell run wsl --install
    • After WSL installs restart computer
    • Open search and look for Ubuntu
    • Follow the instructions to set up your username and password
    • You can now use the Ubuntu shell, to enable copy and paste click the icon in the top left and go to settings and enable copy and paste.
    • Windows <10 users: can use Git Bash, a shell that comes with Git for Windows.
  • Linux users: depending on your specific OS, should be an app called “Shell” or something similar.

Take 3 minutes to (install and) be sure you can open a terminal.

The command line and working directory

  • When you first open the terminal, you should see something like this:
machine_name:~$
  • The command line prompt above contains the following components:
    • machine_name is the name of the computer or host you are using.
    • ~ is a shorthand for your home directory. It indicated that your current working directory is your home directory.
    • The $ is the symbol indicating the command prompt, which shows that the terminal is ready to accept commands. In some systems, the prompt may vary (e.g., # for root users).
    • The blank space after the $ is where you can type your command.
  • For now, focus on working directory: where programs you run through the shell will “operate from”
    • Like opening a file browser window to a particular folder, but also a reference point for programs that read and/or manipulate files.