This tutorial introduces you to the UNIX shell and both basic navigation and advanced uses such as statements and iterations.
Learning outcomes
- Interpret and implement absolute and relative paths in a UNIX hierarchy
- Recognise the various UNIX commands for navigation, creation, manipulation and viewing folders and files in UNIX
- Implement redirection and tab completion tasks
- Execute selection and interation commands in UNIX
- Recognise grep, sed and pipe command structures
- Appreciate the modification of the UNIX shell through profiles and aliases
- Install conda in a UNIX environment and create environments for installing packages
Prerequisites
- It is recommended that you have Notepad++ (Windows) or BBEdit (Mac) for viewing fasta files; most linux default editors can do this.
- It is recommended that you have followed the Concepts in Computer Programming tutorial.
Approximate time to finish tutorial
- UNIX basics worksheet: 3 hours (including installation and set up)
- Conda worksheet: 30 minutes
- UNIX advanced worksheet: 2 hours
Tutorials
UNIX shell tutorial (navigation, creation and viewing)
- A basic undertsanding of UNIX is needed if you wish to do the UNIX-based tasks in the rest of the workshop. I recommend to focus on understanding the contents of this tutorial first.
Conda installation and use
- Conda is very useful for installing programmes used in the UNIX-based tasks in the rest of the workshop. I recommend following this tutorial before doing the others.
Advanced UNIX tutorial
- The contents of this tutorial outline more advanced UNIX shell tasks (i.e. shell programming). A strong understanding of the contents of the first two tutorials is recommended before attempting this tutorial
- Note that understanding this tutorials contents is niot necessary to follow the rest of the workshop, but is recommended if you wish to use UNIX extensively in the future.