Meet the command line: your workbench

Almost every bioinformatics tool you will use is controlled from one place: the command line. Think of it as your workbench, where instead of clicking buttons you get work done by typing short instructions and pressing Enter. It looks bare at first, but it is the most powerful and flexible tool you will learn in this course.

What a shell is

A shell is a program that lets you run tasks by typing commands instead of clicking with a mouse, and the terminal is the window on your screen that shows the shell. When the terminal opens you see a prompt, a short line that often ends in a dollar sign, waiting for you to type a command and press Enter. Bioinformatics lives here because its tools are run by typing, its data files are often enormous, and typed commands can be saved, repeated automatically, and run on powerful shared computers called servers.

Finding your way

The first thing to learn is how to find your bearings. The command pwd, short for print working directory, tells you which folder you are currently sitting in, and ls, short for list, shows you the files and folders inside it.

pwd
ls

/home/maria/bioinfo-course
data  notes.txt  README.md

To move into a folder, use cd, short for change directory. Writing cd data uses a relative path: it means the data folder inside wherever you happen to be right now. You can also give an absolute path such as cd /home/maria/bioinfo-course, which starts from the very top of the computer and works no matter where you currently are.

cd data
ls

reads.fastq  reference.fasta  samples.csv