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An Introduction to UNIX for Cloud Computing

This lesson introduces the UNIX command line to scientists and clinicians who need to use cloud-based and remote computers for basic and biomedical research. The commands used in today's workshop are commonly used by practitioners across disciplines. By practicing the commands, you will gain familiarity with the command line and confidence as a programmer. These commands can be used on a local or remote computer. We hope that you notice an improvement in the speed and reproducibility of your bioinformatics workflow.

Est. Time Lesson name Description
20 mins Introduction Overview of the shell and terminal
20 mins Navigate Navigating files and directories
20 mins Read Reading files
20 mins Work Copying, moving, and deleting files
20 mins Find Files words and files
20 mins Redirect Redirecting outputs and for loops

Learning objectives

In this workshop, you will learn to

  • Understand basic UNIX command structure
  • Navigate through hierarchical directory structures
  • Read, write, create, copy, move, and remove files
  • Understand wildcards and regular expression
  • Redirect outputs and write for loops to build reproducible workflows

A one-page version of this lesson is available here on HackMD. A one-page view of all the code used in this lesson is avilable in the appendix. The lesson materials were adapted from the UC Davis Data Lab's Intro to Cloud Computing workshop, Data Carpentry's Introduction to the Command Line for Genomics lesson, and the Lab for Data Intensive Biology's Advanced Beginner/Intermediate Shell workshop. Please refer to our UNIX Cheatsheet for a list of commonly used commands. The website Explain Shell succinctly explains shell commands and arguments.

The UNIX lesson uses a standardized binder environment, which will work on Windows, Mac, and Linux operating systems, and Firefox, Safari, and Chrome web browsers.

Last update: June 23, 2022