1 Welcome to Shell-Genomics!

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 visual representations of files, folders, applications etc. When using the CLI, you work largely with text representations of files, folders, input and output etc. The shell is a program that presents a command line interface that allows you to control your computer by typing instructions 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 tedius (e.g. testing a range of input parameters) can be simplified.

To use remote computers or cloud computing, you need to use the shell.

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.

Schedule

Setup: Download files required for the lesson

  1. Introducing the Shell

  2. Navigating Files and Directories

  3. Working with Files and Directories

  4. Redirection

  5. Writing Scripts and Working with Data

  6. Project Organization

Finish

References Erin Alison Becker, Anita Schürch, Tracy Teal, Sheldon John McKay, Jessica Elizabeth Mizzi, François Michonneau, et al. (2019, June). datacarpentry/shell-genomics: Data Carpentry: Introduction to the shell for genomics data, June 2019 (Version v2019.06.1). Zenodo.