Introduction to Linux / UNIX and the Bash shell

Welcome to the home page of the First steps with Linux / UNIX and the Bash shell SIB course.

This one-day course provides an introduction to the open source Linux / UNIX operating system, and the Bash shell.

Course material and environment setup 🐣

Course material

• Course slides
• Exercises instructions
• Exercises material
• Exam instructions

Environment setup

The only technical requirement for the course is having a laptop with a reasonably recent version of either a bash shell (version >= 4.0), or a zsh shell (the default shell on Mac OS since 2019). You can display your version of bash with the command bash --version.

• Please read the environment setup instructions for details.
• Make sure to setup your environment before the start of the course.

Course description

Overview 🦉

With the constant evolution of technologies, life scientists such as laboratory biologists are faced with an increasing need for bioinformatics skills to deal with high-throughput data storage, retrieval and analysis.

Although several resources developed for such tasks have a graphical user interface, many operations can be more efficiently handled with command-line programs and utilities.

This course provides an introduction to using the Linux / UNIX operating system via the command line interface (CLI), as well as an introduction to the Bash shell and some of the Linux / UNIX core utilities commands.

More specifically, the course covers the following topics:

• What is Linux / UNIX and why use it?
• Navigating the file system.
• Shell expansions: brace, tilde, and filename expansion.
• File and directory management: create, move, copy, delete.
• File access permissions and ownership.
• Locating files: the find command.
• Displaying file content.
• Archiving and compressing data.
• Standard input/output and pipes.
• Text processing utilities: wc, tr, sort, uniq, cut, diff, cat, paste.
• Introduction to grep and regular expressions.

Audience 📣

This course is addressed to beginners wanting to become familiar with the Linux / UNIX environment, its basic commands, and the Bash shell.

Learning objectives 🎯

At the end of the course you should:

• Be able to execute most of the basic Linux / UNIX commands.
• Be able to build simple pipelines by combining different UNIX commands.
• Be sufficiently skilled for further courses requiring basics of Linux / UNIX, like HPC or NGS courses.

An optional exam can be taken at the end of the course to get a recommendation for 0.25 ECTS credits.

Prerequisites

Knowledge / Skills 💡

This is a course for beginners, no background in Linux / UNIX or any programming language is required.

Technical 💻

A laptop with a command line terminal and a relatively recent version of Bash (>= 4.0).