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Lecture 04: First steps in the shell

Melody Campbell (@melodygcampbell, campbelllab.org)

This lesson introduces you to the command line (a.k.a. Unix shell), which is useful (and necessary) for automating tasks, working with files/directories, and using compute clusters.

In the first lecture, I will describe the history of and larger context for why we want to use the command line. Here are the slides, and if you missed the lecture here is a recorded version.

If you want a second opnion or want to learn cluser-based computing and paralleization, here is a recorded version covering related material by Erick Matsen in 2020.

Learning objectives

After these two lectures, you should be able to:

  • Navigate a file system in the shell (lecture 04)
  • Run commands in the shell (lecture 04)
  • Understand basic usage of redirection (lecture 04)
  • Write a for loop (lecture 05)
  • Edit a file using vim (lecture 05)
  • Write a basic shell script (lecture 05)

Class materials

  • All instructions for this lesson are links or are available in this repository.
    • See the Tutorial section in the next lecture to get started with the exercises.
    • The recorded lecture and introductory slides are linked to above.

Setup: Accessing a Command Line

This material requires access to a unix shell. Different "flavors" of shell have slight variations in commands available so don't be surprised if some of the commands and options are slightly different (especially on OS X).

  • Use a Command Line via Visual Studio Code (recommended)

  • Use a Command Line on Mac OS X

    • Macintosh operating systems are built on Unix, so many of the tools you’ll need are pre-installed on your computer. You can access the command line through an application called Terminal. You can either search for this in Finder, or use the Go drop-down menu to locate it in the Utilities folder.

  • Use a Command Line on Windows 10

    • Windows 10 comes with a new feature called Windows Subsystem for Linux (WSL) that allows you to access Unix tools on your computer. Please install WSL with the instructions here.

Reminders

  • Homework 2 (command line) will be available here on October 13th; it may be useful to reference these questions as you work through material in the second class.

Further references