Accelerate with Automation - Making your code work for you
| Audience | Computational skills required | Duration |
|---|---|---|
| Biologists | Beginner bash | 2-3 hour workshop (~2-3 hours of trainer-led time) |
Description
This repository has teaching materials for a 3 hour, hands-on Intermediate bash workshop led at a relaxed pace. Many tools for the analysis of big data require knowledge of the command line, and this workshop will build on the basic skills taught in the The Foundation - Basic Shell workshop to allow for greater automation using scripts.
Learning Objectives
- Define what a variable is and store information using variables
- Distinguish between variables and positional parameters
- Create a script to run multiple commands as a single command
- Implement loops, positional parameters and variables in a bash script
- Learn about slurm arrays for automation on a high performance computing cluster
These materials are developed for a trainer-led workshop, but are also amenable to self-guided learning.
Contents
| Lessons | Estimated Duration |
|---|---|
| Setting up | 15 min |
Shell scripts and for loops |
75 min |
| Positional parameters | 45 min |
| Slurm arrays | 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.