The shell is a program that presents a command line interface which allows you to control your computer using commands entered with a keyboard instead of controlling graphical user interfaces (GUIs) with a mouse/keyboard combination.
There are many reasons to learn about the shell.
Getting Started
Data Carpentry’s teaching is hands-on, so participants are encouraged to use their own computers to ensure the proper setup of tools for an efficient workflow.
These lessons assume no prior knowledge of the skills or tools.Prerequisites
Workshop participants should follow the instructions on the workshop homepage to set up their computers. For this lesson, you will need a Bash shell and this file.
| Setup | Download files required for the lesson | |
| 00:00 | 1. Introducing the Shell |
What is a command shell and why would I use one?
How can I move around on my computer? How can I see what files and directories I have? How can I specify the location of a file or directory on my computer? |
| 00:30 | 2. Navigating Files and Directories |
How can I perform operations on files outside of my working directory?
What are some navigational shortcuts I can use to make my work more efficient? |
| 01:20 | 3. Working with Files and Directories |
How can I view and search file contents?
How can I create, copy and delete files and directories? How can I control who has permission to modify a file? How can I repeat recently used commands? |
| 02:05 | 4. Redirection |
How can I search within files?
How can I combine existing commands to do new things? |
| 02:50 | 5. Writing Scripts | How can we automate a commonly used set of commands? |
| 03:30 | 6. Project Organization |
How can I organize my file system for a new bioinformatics project?
How can I document my work? |
| 04:00 | Finish |
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.