Introduction to shell (bash)

Audience	Computational Skills	Prerequisites	Duration
Biologists	Beginner/Intermediate	None	1-day workshop (~6 hours of trainer-led time)

Description

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).

Contents

Lessons	Estimated Duration
Introduction to the shell	70 min
Searching and redirection in shell	45 min
Introduction to the Vim text editor	30 min
Shell scripts and for loops	75 min
Permissions and environment variables	50 min

Dataset

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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.

• Some materials used in these lessons were derived from work that is Copyright © Data Carpentry (http://datacarpentry.org/). All Data Carpentry instructional material is made available under the Creative Commons Attribution license (CC BY 4.0).