About this course

An introduction to the Linux command line for people who work on a shared server, written for a Master's level bioinformatics course.

Who it is for

You are comfortable using a computer but have never used a command line. You have a biology background rather than a computing one. And you will be doing your work on a Linux server that somebody else administers, which you reach over the network from your own laptop.

That last point shapes everything here. It means you do not choose the distribution, you will not have administrator rights, your jobs need to outlive an unreliable connection, and your first real task is usually to get data onto the machine and run a tool over it. Most introductions assume the opposite on every one of those points.

How to use it

Work through Start here in order. The sections build on each other, and terms are introduced in the order you meet them. Each lesson has an exercise, and a quiz question whose answer stays hidden until you ask for it — try to answer before you look, because recalling something is what makes it stick.

Type the commands rather than copying them. It is slower, and it is how the shapes of commands end up in your fingers.

The later tiers are not required reading. Going Further covers things you will want eventually, such as software installation and monitoring. Under the Hood explains how Linux is put together, and Networking is a reference for when you need it. Neither is needed to be productive on the command line. Both cover subjects far larger than the room given to them here, so each of their sections ends with a note saying what was left out and where it is covered properly.

What is different from the original

This is an edited version of Linux Journey, not a copy. The main changes:

• The course opens with connecting to a server rather than with choosing and installing a distribution.
• Tab completion, text editing with nano, and Ctrl-C all moved to the beginning, since they are needed on day one.
• New material on ssh, VS Code over ssh, quoting and filenames, shell scripting, conditionals, running many jobs, screen, monitoring with htop, PATH, installing software with conda, disk space, and downloading data.
• grep, sed and awk are given a good deal more room, and the examples use tabular data rather than lists of animals.
• The vim and emacs section was removed. Between nano and VS Code you have everything this course needs.
• A number of factual errors in the original have been corrected, and several have been offered back upstream.

Found a problem?

Anything wrong here is far more likely to come from the changes made in this version than from the original course, so please report it at the issue tracker. Corrections, unclear explanations and broken examples are all worth reporting — if something confused you, it confused somebody else too.