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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


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.

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  • HTML 97.8%
  • Shell 1.7%
  • CSS 0.5%