Advanced Bash scripting Home

Welcome to the home page for the CBRS Advanced Bash Scripting short course on May 8, 9am - 1pm!

This 4 hour, 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

Time permitting we'll look at some Advanced text manipulation from the Intermediate Unix course.

Resources

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. Our 2024 "Summer school" lineup is here: https://site.research.utexas.edu/cbrs/classes/big-data-in-biology-summer-school/2024-summer-school/. Especially popular are:

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