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
• FAQ - a list of questions asked during previous instances of the course.

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 are shells and core utilities, and why use them ?
• Connecting to remote servers with ssh (not covered in details)
• Filesystem overview and navigation: ls and cd
• Basics of the bash shell syntax
• Shell command history and help: history, man
• Filename expansion (globbing)
• File and directory management: mkdir, mv, cp, rm, rmdir
• File access permissions and ownership
• Locating files: find
• Displaying file content: head, tail, cat, less, wc
• Archiving and compressing data: tar and gzip
• Standard input/output and pipes
• Text processing utilities: tr, sort, uniq, cut, cat and 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).