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Bash

NOTE: This area is here for archive purposes only. The current section can be found here.

Bash is the most common programming language in a Unix-like environment these days. More importantly, bash is very likely the most foundational skillset you can learn for bioinformatics (and much more). Below is a table of some quick terminology for some help in what is meant by terms like “bash” and “Unix”. An introduction to bash can be found here. And if you would like some help getting a bash environment up and running on your computer, check out this page 🙂

Some terminology

Here are some terms that are often used interchangeably – not because it’s important to remember them or any differences (it’s not for most of us), but just to have them laid out somewhere.

Term	What it is
shell	what we use to talk to the computer; anything where you are pointing and clicking with a mouse is a Graphical User Interface (GUI) shell; something with text only is a Command Line Interface (CLI) shell
command line	a text-based environment capable of taking input and providing output
Unix	a family of operating systems
bash	the most common programming language used at a Unix command-line

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All bash pages

• Getting a bash environment
• Intro to bash
• Six glorious commands
• The wonderful world of loops
• Why is this all worth it?
• What the heck is my PATH, and how do I get it to do what I want?
• Help installing tools
• Downloading from NCBI
• Other great resources