Bash Scripting Tutorial by Brian Fox

Bash is a powerful programming language that can be used for everything from writing simple scripts to complex programs. This tutorial will give you a solid foundation in Bash so that you can start using it immediately for your own purposes. Bash is a Unix shell, which is a command line interface (CLI) for interacting with the operating system.

It is widely available on many different platforms, including Linux, macOS, and Windows. Bash is an acronym for “Bourne-Again SHell”. The Bourne shell is the original Unix shell created by Stephen Bourne at AT&T Bell Labs in the 1970s.

Bash was created in the 1980s by Brian Fox as a free software replacement for the Bourne shell. Today, Bash is the default shell on most Linux distributions and Apple’s macOS operating system. It is also available on Microsoft Windows 10 through the Windows Subsystem for Linux (WSL).

In this Bash Scripting Tutorial, Brian Fox covers the basics of writing shell scripts. He starts with a brief introduction to the bash shell, including some of its features and capabilities. He then moves on to discussing how to write your own scripts, covering topics such as variables, looping, and flow control.

Finally, he wraps up with a look at some advanced features that can be used in your scripts. Whether you’re new to scripting or just looking for a refresher, this tutorial is a great place to start. It covers all the essentials and provides plenty of examples to illustrate each concept.

With Brian’s clear explanations and practical tips, you’ll be writing shell scripts like a pro in no time!

Bash Command Line Arguments

Most people who are familiar with the Bash shell know that you can pass arguments to commands when invoking them. For example, the ls command takes an argument specifying which directory to list: ls /usr/local/bin

This would list the contents of the /usr/local/bin directory. But what if you wanted to list the contents of multiple directories at once? You could use the -R (recursive) option like this:

ls -R /usr/local/bin /usr/bin However, this would not be very efficient because it would require running the ls command twice. A better way would be to use Bash’s built-in capability for handling command line arguments.

When a Bash script is invoked, it receives as input a list of space-separated arguments. These arguments are available to the script via special variables. The first argument is available in the $1 variable, the second argument is available in $2 , and so on.

So, we could rewrite our previous example like this: #!/bin/bash

ls -R “$1” “$2” This simple script would now work for any number of directories passed as arguments. We just need to make sure that we quote our variables so that Bash doesn’t try to split them on spaces!

Credit: ubunlog.com

What Does [- Z $1 Mean in Bash?

In bash, the [- Z $1] expression tests whether the first argument is an empty string. If it is, then the test returns true; otherwise, it returns false.

Is It Easy to Learn Bash Scripting?

No, bash scripting is not easy to learn. It can be difficult to understand the syntax and get the scripts to work properly. However, with some practice and patience, it is possible to learn how to write bash scripts.

There are plenty of resources available online that can help you get started. Once you understand the basics, you can start writing more complex scripts.

How Do I Write a Bash Script?

Assuming you would like a tutorial on writing bash scripts: A bash script is a file that contains a list of commands to be executed by the command-line interpreter, which is usually invoked as an interactive shell. A bash script can be as simple as a single line that calls an executable, or it can be much more complicated and include loops, conditionals, and functions.

To write a bash script, you first need to open a text editor. If you are using a GUI-based text editor like gedit or Kate, you can create a new file by selecting New from the File menu. In a terminal-based text editor like vim or emacs, you can create a new file by typing :new filename (replacing filename with the name of your file).

Once you have created a new file, you can start typing in your commands. Remember to press Enter after each command to move to the next line. When you are finished entering all of your commands, save the file and close the text editor.

Now that your script is saved, you need to make it executable so that it can be run as a program. To do this, open a terminal and type chmod +x filename (replacing filename with the name of your script). This will give your script execute permissions.

Finally, to run your script, type ./filename (again replacing filename with the name of your script) in the terminal and press Enter. Your script will now be executed!

Why is Bash Used in Bioinformatics?

Bash is a powerful shell that is often used in bioinformatics for a variety of tasks. One of the main reasons bash is so popular in this field is because it can be used to automate many repetitive or complex tasks. For instance, bash can be used to launch multiple jobs on a cluster or grid system, or to process and analyze large data sets.

Additionally, bash provides a rich set of tools for text processing and manipulation, which can be very helpful when working with biological data. Another reason why bash is widely used in bioinformatics is that it is relatively easy to learn compared to other shells. While some knowledge of programming is still necessary, bash syntax is generally straightforward and there are many resources available online to help new users get started.

Finally, bash integrates well with other software tools commonly used in bioinformatics, such as GNU Parallel,awk, and sed.

Brian Fox, Open Source Pioneer, Father of GNU Bash Shell

Conclusion

Bash is a powerful programming language that can be used for everything from writing simple scripts to full-fledged applications. In this Bash scripting tutorial, we’ll cover some of the basics of how to write a Bash script, including variables, functions, and loops. We’ll also touch on some of the more advanced features of Bash, such as running commands in the background and passing arguments to scripts.

By the end of this tutorial, you should have a good understanding of how to write Bash scripts and be able to use them for your own purposes.