Chapter 3. Remedial Unix Shell

The Unix shell is the foundational computing environment for bioinformatics. The shell serves as our interface to large bioinformatics programs, as an interactive console to inspect data and intermediate results, and as the infrastructure for our pipelines and workflows. This chapter will help you develop a proficiency with the necessary Unix shell concepts used extensively throughout the rest of the book. This will allow you to focus on the content of commands in future chapters, rather than be preoccupied with understanding shell syntax.

This book assumes you’re familiar with basic topics such as what a terminal is, what the shell is, the Unix filesystem hierarchy, moving about directories, file permissions, executing commands, and working with a text editor. If these topics sound foreign to you, it’s best to brush up on using more basic materials (see “Assumptions This Book Makes” for some resources). In this chapter, we’ll cover remedial concepts that deeply underly how we use the shell in bioinformatics: streams, redirection, pipes, working with running programs, and command substitution. Understanding these shell topics will prepare you to use the shell to work with data (Chapter 7) and build pipelines and workflows (Chapter 12). In this chapter, we’ll also see why the Unix shell has such a prominent role in how we do modern bioinformatics. If you feel comfortable with these shell topics already, I suggest reading the first section of this ...

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