The Unix operating system has been around since 1969. Back then there was no such thing as a graphical user interface. You typed everything. It may seem archaic to use a keyboard to issue commands today, but it’s much easier to automate keyboard tasks than mouse tasks. There are several variants of Unix (including Linux), though the differences do not matter much for most basic functions.
Increasingly, the raw output of biological research exists as in silico data, usually in the form of large text files. Unix is particularly suited to working with such files and has several powerful (and flexible) commands that can process your data for you. The real strength of learning Unix is that most of these commands can be combined in an almost unlimited fashion. So if you can learn just five Unix commands, you will be able to do a lot more than just five things.
Command-line examples that you are meant to type into a terminal window will be shown indented in a constant-width font, e.g.
ls -lrh
Sometimes the accompanying text will include a reference to a Unix command. Any such text will also be in a constant-width, boxed font. E.g.
Type the
pwdcommand again.
From time to time this documentation will contain web links to pages that will help you find out more about certain Unix commands. Usually, the first mention of a command or function will be a hyperlink to Wikipedia. Important or critical points will be styled like so:
This is an important point!
The lessons from this point onwards will assume very little apart from the following:
In the following documentation, we will also assume that the logged in user has a username ‘ubuntu’ and the home directory is located at /home/ubuntu.