Training: Bash Scripting

The Bash shell is the standard means of interacting with a Linux system, but when combined with many standard Unix system utilities it offers powerful features for scripting analysis tasks and creating simple programs without the need to learn a full programming language. This module expands upon the Bash syntax covered in the ‘Introduction to Linux’ module with discussion of conditional statements, loops, string and integer tests which facilitate the construction of more complex scripts. It also introduces some additional Unix utilities including sort, sed, awk and grep.

This module is recommended for users of the Life Sciences HPC cluster, where bash scripting will allow for more sophisticated automation of analysis tasks.

After completing this module, participants will be able to:

• Create Bash scripts capable of carrying out a number of sequential tasks
• Understand the use of basic programming constructs such as loops and conditional statements
• Sort text files by different fields
• Modify text streams using sed
• Selectively print columns from delimited files using awk
• Identify text matching patterns and regular expressions using grep

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