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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


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.