Summary and Schedule

Command line interface (CLI) and graphic user interface (GUI) are different ways of interacting with a computer’s operating system. They have different pros and cons. Most people are familiar with the GUI as it is the default interface for most software, particularly on Windows and Mac OS. When using the GUI, you see and interact with visual representations of files, folders, applications, and most other functions of your computer. When using the CLI, you work largely with text representations of software, files, folders, input and output. The shell is a program that allows you to control your computer by typing instructions on the CLI with a keyboard.

There are several reasons to learn how to use the CLI:

• For most bioinformatics tools, there are no graphical interfaces. If you want to work in metagenomics or genomics, you’re going to need to use the CLI/ shell.
• The shell gives you power. The command line allows you to work more efficiently. Tasks that are repetitive (e.g. renaming hundreds of files) can be automated. Tasks that are tedious (e.g. testing a range of input parameters) can be simplified.
• To use remote computers or cloud computing, you often need to use the shell.

Getting Started

This lesson assumes no prior experience with the tools covered in the workshop. However, learners are expected to have some familiarity with biological concepts, including the concept of genomic variation within a population. Participants should bring their laptops and plan to participate actively.

This lesson is part of a workshop that 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.

	Setup Instructions	Download files required for the lesson
Duration: 00h 00m	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?
Duration: 00h 30m	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?
Duration: 01h 20m	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?
Duration: 02h 05m	4. Redirection	How can I search within files? How can I combine existing commands to do new things?
Duration: 02h 50m	5. Writing Scripts and Working with Data	How can we automate a commonly used set of commands?
Duration: 03h 30m	6. Project Organization	How can I organize my file system for a new bioinformatics project? How can I document my work?
Duration: 04h 00m	Finish

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

This workshop is designed to be run on pre-imaged Amazon Web Services (AWS) instances. For information about how to use the workshop materials, see the setup instructions on the main workshop page.