Author: Wenbin Guo
Last Update: 2022 Spring
This introductory workshop introduces the Unix command line and shell programming fundamentals, focusing on building practical skills for computational biology and data science. In this workshop, we will learn to utilize essential commands, navigate Unix-based systems, manipulate files, and automate workflows. Additionally, the workshop covers writing and executing basic shell scripts to enhance productivity and reproducibility. For registration information, please refer to this link
The workshop is taught every quarter (3-day workshop, 3 hours per day).
Day 1: Introduction to Unix command line
- Overview of the Unix environment and command-line interface
- Navigating file systems: directories, paths, and file management
- Understanding file permissions and access
- Basic commands for files and folders:
ls,cd,cp,mv,rm,vi,gzip,scp, etc. - Hands-on exercises with command-line basics
Day 2: Advanced Command Line Tools and Text Processing
- Working with file content:
cat,head,sort,cut,count, etc. - Introduction to pipes and redirection (
|,>,<) - Advanced text processing with
sed,awk, andgrep - Pattern matching and regular expressions
- Practical exercises for data manipulation and exploration
Day 3: Shell scripts and submitting jobs on hoffman2
- Variables, operations, loops, and conditionals in shell scripts
- Writing and executing scripts for automation
- Debugging and troubleshooting common script issues
- Submitting and managing jobs on Hoffman2 cluster
Access to a Unix-based system (Linux or macOS) or the Windows Subsystem for Linux (WSL) for Windows users.
No prior experience with Unix or programming is required. Participants should have a Hoffman2 account to use hoffman2 cluster@UCLA
slides: slides for each day of the workshopdayN: example code and exercises for each day’s topics
