Linux

Linux is a family of open-source Unix-like operating systems based on the Linux kernel. It's typically packaged in a distribution, which includes the Linux kernel along with a set of software tools and utilities. There are many different distributions of Linux, such as Ubuntu, Fedora, Red Hat, and CentOS.

In this guide, the "command line" refers to the interface between you and the shell. Checkout the quick reference for common commands.

Concepts

  • Operating System: The software that manages resources of a computer.
  • Architecture: The type of CPU (e.g., x86, x86_64, ARM).
  • Distribution: A version of the Linux operating system.
  • Terminal: The window in which you type commands.
  • Shell: The program that interprets and executes commands.

Important

When creating an instance on AWS, you're setting up a virtual machine that runs an operating system of your choice. For maximum compatibility with our software, use Ubuntu 22.04 LTS (on 64-bit x86).

Terminal

The "terminal" is the interface between you and the shell. It's also referred to as the "command line" or the "console". Various programs can serve as a terminal, such as:

  • iTerm on macOS
  • cmd on Windows
  • EC2 Serial Console
  • The "Terminal" tab in RStudio

Shell

The "shell" is the program that interprets and executes commands. Examples include:

  • bash (most common on Linux systems)
  • zsh (the default on macOS)

Tip

For maintainability and portability, it's recommended to write scripts in bash and be explicit about it. For an interesting discussion on this topic, check out this Stack Overflow post.

Read through the bash guide for more information on the writing and executing shell scripts.

Windows Subsystem for Linux (WSL)

Windows users can run a Linux distribution on Windows using WSL. This allows you to run Linux command-line tools and utilities directly on Windows without needing a virtual machine or dual-boot setup. If you want to use WSL, follow the installation instructions.

Created by Ryan D. Najac for the Palomero Lab at the Institute for Cancer Genetics.
Page last updated on 2024-10-17.