Shell Scripts¶

What is a shell script?¶

A shell script is a text file that contains a series of commands that can be executed by the shell. The shell is a program that interprets and executes commands. The most common shell on Linux is bash.

How to write a shell script¶

To write a shell script, you can use any text editor. The following is an example of a simple shell script:

#!/bin/bash

echo "Hello, world!"
echo "The current date and time is $(date)"

This script will print the message "Hello, world!" to the console.

How to run a shell script¶

To run a shell script, you can use the following command:

bash <script_name>

For example, to run the script above, you would use the following command:

bash hello_world.sh

Variables¶

Variables are used to store data in shell scripts. To declare a variable, you use the following syntax:

variable_name=value

For example, the following code declares a variable named name and assigns it the value "John Doe":

name="John Doe"

You can then access the value of the variable by using its name. For example, the following code will print the value of the name variable:

echo $name

Conditional statements¶

Conditional statements are used to control the flow of execution in shell scripts. The most common conditional statements are if, else, and elif:

The if statement is used to execute a block of code if a condition is met.
The else statement is used to execute a block of code if the condition in the if statement is not met.
The elif statement is used to execute a block of code if a condition is met, but the condition in the if statement is not met.

For example, the following code will print the message "Hello, world!" if the variable name is not empty:

if [ -n "$name" ]; then
  echo "Hello, $name!"
fi

Loops¶

Loops are used to execute a block of code repeatedly. The most common loops are for and while:

The for loop is used to iterate over a list of items.
The while loop is used to execute a block of code as long as a condition is met.

For example, the following code will print the names of all the files in the current directory:

for file in *; do
  echo $file
done

Functions¶

Functions are used to group together a set of commands that can be executed repeatedly. To define a function, you use the following syntax:

function_name() {
  <block of code>
}

For example, the following code defines a function named greet that prints the message "Hello, world!" to the console:

function greet() {
  echo "Hello, world!"
}

You can then call the function by using its name. For example, the following code will call the greet function:

greet

Output redirection¶

Output redirection is used to redirect the output of a command to a file. To redirect output to a file, you use the following syntax:

command > output_file

For example, the following code will redirect the output of the ls command to the file list.txt:

ls > list.txt

Input redirection¶

Input redirection is used to redirect input to a command from a file. To redirect input from a file, you use the following syntax:

command < input_file

For example, the following code will read the contents of the file list.txt and print them to the console:

cat list.txt

Error handling¶

Error handling is used to deal with errors that occur in shell scripts. The most common way to handle errors is to use the try and catch statements:

The try statement is used to execute a block of code.
The catch statement is used to handle errors that occur in the try block.

For example, the following code will try to create a directory named new_dir. If the directory already exists.

Examples of Bash in Bioinformatics¶

Introduction To Bash: Using the Terminal For Bioinformatics. University of Adelaide.
Process fasta script. Pavlo Hrab.
Samtools: faidx

References¶

Created: 05/16/2023: Updated: 05/17/2023

Carlos Lizárraga