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Intermediate bash

Audience Computational skills required Duration
Biologists Beginner bash 2 hour workshop (~2 hours of trainer-led time)


This repository has teaching materials for a 2 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 Introduction to the command-line interface workshop to allow for greater automation. This workshop will include lessons on using the command-line text editor, Vim, to create and edit files, utilizing for-loops for automation, using variables to store information, and writing scripts to perform a series of commands in a sequential order.

Learning Objectives

These materials are developed for a trainer-led workshop, but also amenable to self-guided learning.


Lessons Estimated Duration
Setting up 15 min
Exploring the basics 25 min
Introduction to Vim 25 min
Shell scripts and for loops 75 min


Introduction to Shell: Dataset

Installation Requirements

Mac users: No installation requirements.

Windows users: GitBash