UNIX and Bash basics

This GitHub repository contains some of the most widely-used commands of Bash, a programming language of the UNIX family of operating systems. I bet that I've already lost your attention. No worries, in this brief beginner tutorial we will go through each concept step by step.

One of the most fundamental question now is: why do I need to know Bash? Well, if you are about to pursue a career as a bioinformatician (and if you ended up here, probably you are)... there's no way out. Bash is essential in bioinformatics. Alternatively, why not? Bash is a very handful and practical way to interact with your computer, and allows you to perform several tasks in a very fast way. Once again, you'll find everything out as you go through this tutorial. If it helps, see it as a way to learn a new language: instead of committing to Duolinguo, learn Bash!

🪅 Enjoy! 🪅

And feel free to get in touch!

This GitHub was originally intended to introduce trainee students of the EVO • COM group of the University of Bologna to the UNIX and Bash environments. Of course, this GitHub is freely available to use by anyone who may find it helpful.

What's inside this repository?

Very few files, indeed, but fairly packed. Commands and explanations are presented in markdown files and are divided into macro-topics. They are numbered in the order I tipically use when training students. A series of example files are also provided.

Macro-topic	Description
01 - Bash basics	The very first introduction to Bash for bioinformatics. Look here for basic Bash commands and operations.
02 - Working with Conda	What is Conda and how to use it.
03 - Working with screen sessions	What is a screen session and how to use it.
04 - git and GitHub	What is git and how to use it.
Example files/	A directory containing several files used to test commands.
download_PDFs/	A directory containing the PDF version of markdown files to be downloaded