Intro to Linux and Bash

Learning Objectives

Learning Objectives:

Connect to a remote computer cluster

Navigate the Linux file system using the BASH shell

Manipulate files and directories

Modify file ownership and permissions

Use multiple strategies to get help and problem solve

Ask questions about the status of the system

Move files between computers

Work with file compression

Inspect files

Use regular expressions with sed and grep

Pipe inputs and outputs

Resources:

• BASH reference manual
• Advanced BASH scripting guide
• Brandies, P. A., & Hogg, C. J. (2021). Ten simple rules for getting started with command-line bioinformatics. PLoS Computational Biology, 17(2), e1008645.
• Alnasir, J. J. (2021). Fifteen quick tips for success with HPC, ie, responsibly BASHing that Linux cluster. PLOS Computational Biology, 17(8), e1009207.
• BASH one-liners