lecture09

Lecture 9: First steps in the shell

Erick Matsen (@ematsen, matsen.group)

Learning objectives

After this course, you should be able to:

• Navigate a file system in the shell
• Run commands in the shell
• Understand basic usage of piping and redirection
• To be able to edit a file using vim
• To write a basic shell script
• To be able to run a command in parallel using GNU Parallel

Class materials

Everything you need is in this repository.

Tutorial

 _______     _______.  ______     ___      .______    _______
|   ____|   /       | /      |   /   \     |   _  \  |   ____|
|  |__     |   (----`|  ,----'  /  ^  \    |  |_)  | |  |__
|   __|     \   \    |  |      /  /_\  \   |   ___/  |   __|
|  |____.----)   |   |  `----./  _____  \  |  |      |  |____
|_______|_______/     \______/__/     \__\ | _|      |_______|

.___________. __    __   _______
|           ||  |  |  | |   ____|
`---|  |----`|  |__|  | |  |__
    |  |     |   __   | |   __|
    |  |     |  |  |  | |  |____
    |__|     |__|  |__| |_______|

     _______. __    __   _______  __       __
    /       ||  |  |  | |   ____||  |     |  |
   |   (----`|  |__|  | |  |__   |  |     |  |
    \   \    |   __   | |   __|  |  |     |  |
.----)   |   |  |  |  | |  |____ |  `----.|  `----.
|_______/    |__|  |__| |_______||_______||_______|

This is an interactive tutorial to teach you about navigating the shell. For reference you might be interested in the excellent course material put out by Software Carpentry.

To get started, execute the following commands in your shell:

ssh rhino
git clone https://github.com/fredhutchio/tfcb_2019.git
cd tfcb_2019/lectures/lecture09

Now you can start the first lesson by clicking on the first-steps.md link in the file list above and starting your adventure!

If you have problems at any point, flag us down and we'll come by to help out.