Command line interface (OS shell) and graphic user interface (GUI) are different ways of interacting with a computer’s operating 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.
A lot of genomics analysis is done using command-line tools for three reasons:
- you will often be working with a large number of files, and working through the command-line rather than through a graphical user interface (GUI) allows you to automate repetitive tasks,
- you will often need more compute power than is available on your personal computer, and connecting to and interacting with remote computers requires a command-line interface, and
- you will often need to customize your analyses, and command-line tools often enable more customization than the corresponding GUI tools (if in fact a GUI tool even exists).
This lesson assumes no prior experience with the tools covered in the module. 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 uses an Amazon Machine Instance (AMI). If you are attending a tutor-led workshop your AMI will be created for you and will be sent the log in information you will need for this lesson. If you are self-studying Prenomics, you will need to set up your own instance using our Create Your Own AWS Instance module.
Before starting this lesson, you should go through the Files and Directories lesson.