BASH scripting

Bourne-Again Shell (Bash)

Bash is an acronym for "Bourne-Again Shell", the name of a code interpreter and a high-level programming language, and it is a must-know tool in Computational Chemistry and Biology. You can use Bash scripting in Unix/Linux computers through a terminal. When you initialize the shell, i.e, the interpreter, your computer runs initialization files -- ~/.bash_profile, ~/.bash_login, and ~/.profile (where ~/ points to your home directory) -- but we do not recommend changing these files unless you really know what you are doing. In most cases, you can change the ~/.bashrc file, which allows the user to customize the system according to their needs.

A bash script is a text file containing a series of instructions written in the bash language. You can create one by typing the following commands in the terminal:

 touch my_first_script.sh

which will generate a modifiable file that you can use to write the instructions to be executed by the shell. You can use the Vi text editor to write your code; just remember to add to the beginning of the file the following line:

 #!/bin/sh

This line tells the interpreter that this is a bash script. You can run your script by telling the interpreter:

 bash my_first_script.sh

or you can change the permissions of the file to make it an executable by typing:

 chmod +x my_first_script.sh

and then running:

 ./my_first_script.sh

Environment Variables

Bash allows the user to assign values to variables in the command line, but