This workshop is part of the Fall 2022 Workshop series of the McGill initiative on Computational Medicine. The initiative was formed in 2017 and aims to deliver inter-disciplinary research programs and empower the use of data in health research and health care delivery.
This workshop is aimed at people with little or no programming experience who want to get familiar with the UNIX command line and shell scripting. We will cover the structure of the UNIX operating system, basic file management operations, useful built-in commands and text processing. At the end of the workshop you should feel comfortable opening a terminal, creating files, accessing directories, running basic commands and processing simple text files. This session is designed with a strong hands-on component and we will encourage students to participate in solving interesting programming challenges.
- Being confortable managing files in a computer using a file manager
- Have access to a UNIX terminal.
- Mac OS and any linux distribution will have a terminal already
- Mac OS: search for terminal in your spotlight search
- Windows users:
- Option 1 **recommended: Download a unix subsystem (WSL)
- Option 2:Download MobaXterm
- Mac OS and any linux distribution will have a terminal already
- Introduction to UNIX
- Introduction to the UNIX operating system
- Files and processes
- Directory Structure
- The Terminal
- Basic commands and managing files
- Basic Commands
- Directory Management
- File Management
- Redirecting output
- File permissions
- Hands on 1 exercise
- Text Processing
- Pipes
- Basic text processing commands
- Pattern matching with grep
- Pattern substitution with sed
- Hands on 2 exercise
- UNIX Variables
For scripting:
For HPC:
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Datasets https://perso.telecom-paristech.fr/eagan/class/igr204/datasets
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The material given in this course is a compilation of different sources:
Workshop created as part of the McGill Initiative in Computational Medicine