Week 3: Unix shell basics

Author

Affiliations

Jelmer Poelstra

CFAES Bioinformatics Core, Ohio State University

Dept. of Plant Pathology, Ohio State University

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Overview

This week only has a single lecture, because Monday is Labor Day. It will be the first of two weeks focused on introducing you to the Unix shell, which is a powerful command-line interface that you’ll be using extensively throughout the course.

Learning goals & lectures

A) Unix shell basics (Wednesday)

• What the Unix shell is and what you can do with it.
• Why it can be beneficial to use a command-line interface in general, and the Unix shell specifically.
• How Unix commands are structured.
• What environment variables are and how to print their values.
• How to navigate around your computer with Unix commands.

Assignments & exercises

• Graded Assignment 1 (GA1): Markdown and shell basics (Due 9/13)

Readings

No required readings this week.

Optional self-study material

• Allesina and Wilmes (2019) — Chapter 1: Unix (OSU library link )

References

Allesina, Stefano, and Madlen Wilmes. 2019. Computing Skills for Biologists: A Toolbox. Princeton University Press. https://doi.org/10.1515/9780691183961.