Introduction to the command line interface (shell/bash/Unix/Linux)

Audience Computational skills required Duration
Biologists None 1-day workshop (~6 hours of trainer-led time)


This repository has teaching materials for a 1-day Introduction to shell workshop. This workshop focuses on teaching basic skills to use the command line interface, specifically bash, the lessons include for loops, shell scripting, positional parameters. This workshop is a prerequisite to a workshop on RNA-seq analysis.

These materials were developed for a trainer-led workshop, but are also amenable to self-guided learning.

Learning Objectives

  1. Understand the necessity for, and use of, the command line interface (bash/shell).


Click here for links to lessons and the suggested schedule

Installation Requirements

Mac users: No installation requirements.
Windows users: GitBash


Introduction to Shell: Dataset

These materials have been developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC). These are open access materials distributed under the terms of the Creative Commons Attribution license (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.