Command Line Introduction
==================================================================================================

**What is the command line?**

A user interface to all operations of your computer. 

   - All programs you use on a regular basis are really just user interfaces to more easily call actions on the command line!
   - Anything you normally do on your computer could be done directly through the command line.
   
Can also be refered to as bash, shell or terminal.

**Why do you need to use the command line for bioinformatics?**

   1. Actions are reproducible, sharable as scripts, and *generally* consistent across platforms.
   2. Many bioinformatics tools can only be run directly from the commnd line.
   3. Many tasks are easier and can run more efficiently...
      
	  - Editing and moving files
	  - Performing repetetive tasks
	  - Acting on very large files that cannot open with other programs

**Rule Number 1: "With great power comes great responsibility, think before you type!"**

The command line is a *very powerful* tool, and thus could cause a *lot* of problems if you aren't careful.

Don't be scared, but also don't be sloppy. 

   - One particular line of code could wipe every personal file off your computer permanantly...
   - However, consequences of this magnitude are highly unlikely. Usually commands will just fail...
   - Just remember there is no ctrl-z to undo actions on the command line.
      - And be extra careful with the **rm** command, it deletes files and folders with no way to recover.

Navigation
--------------------------------------------------------------------------------------------------

**How do you move around in the folder hierarcy of your computer?**

.. figure:: ../images/folder_hierarchy.jpg
   :scale: 60 %
   :alt: folder_hierarchy 
   
   Source: https://www.linuxtrainingacademy.com/linux-directory-structure-and-file-system-hierarchy/

We will learn some things and stuff


What is the terminal?
---------------------




Basic Commands
--------------


.. code-block:: python

   for i in (1..100)
   do
      echo $i
   done