Basic Shell
| Audience | Computational skills required | Duration |
|---|---|---|
| Biologists | None | 2-3 hour workshop (~3 hours of trainer-led time) |
Description
This repository has teaching materials for a 2-3 hour, hands-on Basic Shell workshop led at a relaxed pace.
Learning Objectives
- Recognize the importance of shell in the analysis of high throughput sequencing (HTS) data
- Install and locate the software/tools necessary for accessing the shell
- Describe the organization of the file directory and how to move through it
- Demonstrate different ways to manipulate files, such as moving, copying, and renaming
- Compare different commands for examining small or large files
- Create new files and make edits to existing files with nano
- Contrast shell scripts with direct commands
These materials are developed for a trainer-led workshop, but also amenable to self-guided learning.
Contents
| Lessons | Estimated Duration |
|---|---|
| Introduction and Why Shell? | 15 min |
| Acessing the Shell | 15 min |
| Moving around and basics | 60 min |
| Creating Files and Searching | 30 min |
| Shell Scripts | 20 min |
| Wrap-up | 15 min |
Dataset
Introduction to Shell: Dataset
Installation Requirements
Mac users: No installation requirements.
Windows users: GitBash
Resources
- Shell cheatsheets:
- Explain shell - a web site where you can see what the different components of a shell command are doing.
- Software Carpentry tutorial: The Unix shell
- Introduction HOW-TO Bash
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.