Introduction to Shell¶
Command line interface (CLI) and graphic user interface (GUI) are different ways of interacting with a computer's operating system. They have different pros and cons. Most people are familiar with the GUI as it is the default interface for most software, particularly on Windows and Mac OS. When using the GUI, you see and interact with visual representations of files, folders, applications, and most other functions of your computer. When using the CLI, you work largely with text representations of software, files, folders, input and output. The shell is a program that allows you to control your computer by typing instructions on the CLI with a keyboard.
There are several reasons to learn how to use the CLI:
- For most bioinformatics tools, there are no graphical interfaces. If you want to work in metagenomics or genomics, you're going to need to use the CLI/ shell.
- The shell gives you power. The command line allows you to work more efficiently. Tasks that are repetitive (e.g. renaming hundreds of files) can be automated. Tasks that are tedious (e.g. testing a range of input parameters) can be simplified.
- To use remote computers or cloud computing, you often need to use the shell.
| Lesson | Overview |
|---|---|
| Pre . Unix, Linux and UNIX Shell | Quick overview on UNIX operating system and it's importance |
| 1. Introducing the shell | Introduce cd ls |
| 2. Navigating files and directories | moving around the filesystem. Introduce absolute vs relative path |
| 3. Working with files and directories | View, search within, copy, move, and rename files. Create new directories |
| 4. Redirection | Employ the grep command to search for information within files |
| 5. Writing scripts and working with data | How to use a terminal based text editor |
| 6. Project Organisation | Create a file system for a bioinformatics project |
Getting Started
This lesson assumes no prior experience with the tools covered in the workshop. However, learners are expected to have some familiarity with biological concepts, including the concept of genomic variation within a population. Participants should bring their laptops and plan to participate actively.
Attribution Notice
- This workshop material is adapted and inspired by Data Carpentry - Shell Genomics
License
Genomics Aotearoa / New Zealand eScience Infrastructure "Intermediate Shell for Bioinformatics" is licensed under the GNU General Public License v3.0, 29 June 2007 . (Follow this link for more information)