The shell I

The shell, or the command line interpreter, is a very important program in bioinformatics work. Therefore, spending some time learning how to use this tool is well worth it.

There are many different shells available, and most systems have more then one installed. Bash, or the "Bourne Again Shell", is the default shell on many GNU/Linux and Mac OSX systems. You can examine which shell you are using by executing the following command:

[mtop@albiorix ~]$ echo $SHELL
/bin/bash
[mtop@albiorix ~]$ 

Here we are using the program echo, that is used to echo things to the screen, to display the value of the variable SHELL. We will be using both echo and environmental variables much more in the future exercises.