Introduction to the Command Line for Genomics

Command line interface (OS shell) and graphic user interface (GUI) are different ways of interacting with a computer’s oprating system. The shell is a program that presents a command line interface which allows you to control your computer using commands entered with a keyboard instead of controlling graphical user interfaces (GUIs) with a mouse/keyboard combination.

There are quite a few reasons to start learning about the shell:

For most bioinformatics tools, you have to use the shell. There is no graphical interface. If you want to work in metagenomics or genomics you’re going to need to use the shell.

The shell gives you power. The command line gives you the power to do your work more efficiently and more quickly. When you need to do things tens to hundreds of times, knowing how to use the shell is transformative.

To use remote computers or cloud computing, you need to use the shell.

Getting Started

Data Carpentry’s teaching is hands-on, so participants are encouraged to use their own computers to ensure the proper setup of tools for an efficient workflow.
These lessons assume no prior knowledge of the skills or tools.

Prerequisites

This lesson uses data hosted on an Amazon Machine Instance (AMI). Workshop participants will be given information on how to log-in to the AMI during the workshop. Learners using these materials for self-directed study will need to set up their own AMI. Information on setting up an AMI and accessing the required data is provided on the Genomics Workshop setup page.

For Instructors

If you are teaching this lesson in a workshop, please see the Instructor notes.

Schedule

	Setup	Download files required for the lesson
13:00	1. Introducing the Shell	What is a command shell and why would I use one? How can I move around on my computer? How can I see what files and directories I have? How can I specify the location of a file or directory on my computer?
13:30	2. Navigating Files and Directories	How can I perform operations on files outside of my working directory? What are some navigational shortcuts I can use to make my work more efficient?
14:00	3. Working with Files and Directories	How can I view and search file contents? How can I create, copy and delete files and directories? How can I control who has permission to modify a file? How can I repeat recently used commands?
14:45	4. Coffee Break	Break
15:00	5. Redirection	How can I search within files? How can I combine existing commands to do new things?
15:40	6. Writing Scripts and loops	How can we automate a commonly used set of commands?
16:20	7. Project Organization	How can I organize my file system for a new bioinformatics project? How can I document my work?
16:30	Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.