TOPIC: Unix
None! This is where it all begins 🙂
- Lesson 1: An introduction to the Unix-like command-line
- Lesson 2: An introduction to package and environment management with Conda
Getting familiar with working at a "Unix-like" command line is one of the most foundational skillsets we can develop for bioinformatics (and much more than bioinformatics).
Many of the most common bioinformatics approaches these days happen in this text-based environment, and having a solid foundation here can make everything we're trying to learn and do much easier. This Unix Crash Course at Happy Belly Bioinformatics holds a set of 5 introductory, heavily annotated tutorials to help us get from being completely new to this wonderful world up to being great friends with it 🙂
Date posted: 11 April 2020
Author(s): Dr. Michael D. Lee
Instructor(s): Dr. Benjamin Tully
- Accessing our Unix-like environment
- Some general rules
- Running commands and general syntax
- File-system structure and how to navigate
Content | Video presentation |
Date posted: 11 April 2020
Author(s): Dr. Michael D. Lee
Instructor(s): Dr. Benjamin Tully
- Working with files
- What a plain-text file is
- Introduction to a command-line text editor: nano
- Working with directories
Content | Video presentation |
Date posted: 11 April 2020
Author(s): Dr. Michael D. Lee
Instructor(s): Dr. Benjamin Tully
- Redirectors
- Wildcards
- History
Content | Video presentation |
Date posted: 12 April 2020
Author(s): Dr. Michael D. Lee
Instructor(s): Dr. Benjamin Tully
- Here we’re going to touch upon 6 glorious commands that are absolutely worth having in our toolkit!
Content | Video presentation |
Date posted: 12 April 2020
Author(s): Dr. Michael D. Lee
Instructor(s): Dr. Benjamin Tully
- Variables
- For loops
Content | Video presentation |
Date posted: 9 May 2020
Author(s): Dr. Michael D. Lee
Instructor(s): Dr. Benjamin Tully
Conda is a package and environment manager that is by far the easiest way to handle installing most of the tools we want to use in bioinformatics. This lesson covers the fundamentals of installing and using Conda.