Introduction to Command-line and Shell Scripts

Overview

This workshop provides practical training in command-line and shell programming. Students will:

• Learn how to navigate and manage the file system in a Unix environment
• Gain practical experience with advanced command-line tools and HPC clusters
• Develop skills in writing shell scripts to automate workflows
• Apply command-line techniques to real-world computational tasks

For registration, visit the QCBio workshop page.

Prerequisites

• No prior Unix or programming experience required
• Access to a Unix-based system (Linux, macOS, or WSL on Windows)

Textbooks

• “Linux Command Line and Shell Scripting Bible” by Richard Blum and Christine Bresnahan
• “Bash Cookbook” by Carl Albing and JP Vossen

Grading

• Quiz: 20%
• Assignments: 70%
• Participation: 10%

Schedule

Date	Topic	Materials
Day 1	Introduction to Unix Systems and the Command Line An introduction to the Unix environment, file system, and command-line basics.	Slides Data
Day 2	Advanced Command-line Tools Using tools such as vi, grep, sed, awk, and pipes to process files and analyze data.	Slides Data
Day 3	Shell Scripting and Workflow Automation Writing shell scripts, automating repetitive tasks, and submitting jobs on HPC systems.	Slides Data