A Beginner's Guide to Bash for biologists: Unleash the Power of the Command Line

Introduction

With the recent rise in the availability of genomic data, there is need for more biologists to use advanced computer programmes to analyse data. Many of these programs/tools run on the command line running the Bash shell.  Short for "Bourne Again Shell," Bash is a command-line interface (CLI) that allows users to interact with their computer or server through text-based commands. While it might seem intimidating at first, Bash is an invaluable tool for beginners and experts alike. In this beginner's guide, we'll introduce you to Bash and help you take your first steps towards harnessing its potential.

What is Bash?

Bash is a command interpreter that allows users to interact with their computer's operating system by typing commands into a terminal or shell prompt. It's the default shell for most Unix-based operating systems, including Linux and macOS. Windows users can now access bash with Windows Subsystem for Linux (WSL).. Bash is a free and open-source software, making it accessible to anyone interested in learning how to use it.

Why Learn Bash?

Learning Bash offers numerous advantages, even for beginners:

1. Efficiency:

Bash can execute tasks more quickly and efficiently than graphical user interfaces (GUIs). Once you become proficient, you'll be able to perform complex operations with just a few keystrokes. Bash comes in handy when carrying out operations on a large dataset. e.g. calling variants for a few thousand samples.

2. Automation:

Bash allows you to write scripts, which are sets of commands that can be executed automatically. This is incredibly useful for automating repetitive tasks, such as file management or system maintenance.

3. Scripting:

Bash scripting is a valuable skill for anyone interested in computational biology. Many biologists utilise bash scripts to perform complex analyses by adding together a few simple bash commands.

4. Portability:

The skills you learn in Bash are highly transferable. Bash scripts and commands can be used across different Unix-based systems, providing you with valuable knowledge and experience.

Getting Started with Bash

1. Accessing the Terminal:

To start using Bash, you'll need to access the terminal or command prompt on your system. On Linux and macOS, you can usually find it by searching for "Terminal" or "Shell" in your applications. On Windows, you can use the built-in Command Prompt or install a Bash emulator like Git Bash or Windows Subsystem for Linux (WSL).

2. Basic Commands:

Here are some fundamental Bash commands to get you started:

pwd : Print the current working directory.

ls : List files and directories in the current directory.

cd  : Change the current directory.

mkdir : Create a new directory.

touch : Create a new empty file.

cp : Copy files or directories.

mv : Move or rename files or directories.

rm : Remove files or directories.

3. Navigating the File System:

Understanding how to navigate the file system is crucial. You'll use commands like cd, ls, and pwd to move around and explore your system's directories.

4. Getting Help:

If you ever get stuck or need information about a command, you can use the man command followed by the command you want to learn more about. For example, man ls will display the manual page for the ls command.

Conclusion

Bash is a powerful tool that can greatly enhance your efficiency and productivity when working with computers and servers. While it may take some time to become proficient, the investment is well worth it. As you continue to learn and explore, you'll discover the vast capabilities of Bash, including scripting, automation, and system administration.

In future articles, we'll delve deeper into Bash scripting exploring ways you can get started to use bash to perform simple tasks. Bash is a versatile and rewarding skill to add to your toolbox as you embark on your journey into the world of command-line computing.