Advanced Bash scripting Home
Welcome to the home page for the CBRS Advanced Bash Scripting short course 9am - noon on Wednesday May 7 and Friday May 9.
This hands-on short course will cover advanced topics in writing bash shell scripts, providing tips, examples and best practices for creating robust "pipeline scripts" that execute multiple processing steps. Topics include defining functions, argument processing and defaulting, subtleties of Unix stream and text manipulation, and error checking. We will also explore effective use of Unix tools such as cut, sort, read, awk, grep, sed, and perl.
Course Outline
- Getting Started
- Introduction
- Basic command-processing script
- Stream handling
- Shells and sub-shells
- Error handling
- Finally, we'll look at some Advanced text manipulation from the Intermediate Unix course.
Resources
- Wikis for CBRS Intro and Intermediate Unix courses:
- Some Linux Commands (Intro Unix course)
- Review of Linux basics (Intermediate Unix course)
- Advanced text manipulation (Intermediate Unix course)
For more Linux practice in the context of bioinformatics analyses, the CBRS offers 4 or 5 half-day workshops with lots of hands-on experience. See the CBRS 2025 "Summer school" schedule: https://site.research.utexas.edu/cbrs/classes/big-data-in-biology-summer-school/2025-summer-school/.
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Advanced Bash scripting Home contributed May 04, 2025
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Error handling contributed May 04, 2025
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Basic command-processing script contributed May 01, 2025
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