Introduction to Linux / UNIX and the Bash shell - UNIL CAS in Data Stewardship

Welcome to the home page of the Introduction to Linux / UNIX and the Bash shell course of the University of Lausanne CAS in Data Stewardship.

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

🔥 Important: this course requires participants to prepare before the in-person class. Please make sure to:

• Set up your environment.
• Complete the pre-course tasks.

Course material and environment setup 🐣

Course material

• Course slides (PDF)
• Exercise instructions
• Exercise material (.zip)
• Exam instructions

Environment setup

The only technical requirement for the course is a laptop with a bash shell (version >= 4.0) or a zsh shell (the default shell on macOS since 2019) installed.

• You can display your version of bash with the command: bash --version
• Please read the environment setup instructions for details. Make sure to set up your environment before the start of the course.

Course description 🦉

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 commands.

More specifically, the course covers the following topics:

• What is Linux / UNIX and why use it ?
• Navigating the filesystem.
• 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.

Course structure 🌱

Due to limited in-class time (0.5 days), this course requires participants to self-study before and after the class.

Pre-course tasks

We kindly ask you to complete the following tasks before the course:

• Set up your environment (~0.5h).
• Complete chapters 1 to 4 of the SIB UNIX fundamentals e-learning module (~3h):
  • Chapter 1: What is UNIX / Linux
  • Chapter 2: The UNIX filesystem
  • Chapter 3: UNIX shell - first steps
  • Chapter 4: UNIX shell - filesystem commands
• Complete exercises 1 and 2 of the course exercises (~1h).
  • For exercise 1, please also complete the Additional task sections.
  • For exercise 2, the Additional task sections are optional.

On-site course

During the in-class part of the course, the following topics will be covered.

• Theory presentation (course slides).
• Exercises 3, 5, and 7A.

Post-course tasks

Exercises to do on your own, after the class.

• Exercises 4, 6, and 7B (~2h).
• The Additional task sections of the exercises are optional.