***********************************
Intro to the bash shell
***********************************

Intro and Objectives
====================

You will learn how to use the bash shell - a very common command line
interface on Linux systems. Why learn the bash shell?

* Many Linux tasks rely on you being a competent bash shell user
* Massive efficiency and productvity gains possible using bash
* Gets you closer to the computer and increases your technical sophistication
* Reinforces notion of functional decomposition - little programs that do one thing well

You will learn to use the bash shell to do (among other things):

* navigation through the file and folder structure on your computer
* file and folder manipulation (create, delete, move, copy)
* run programs
* get information about your computer system
* use pipes and filters to accomplish file management tasks by combining multiple shell commands
   
Readings
========

* `Tech Support Cheat Sheet <https://xkcd.com/627/>`_

* Read Sections 1-4 of the Software Carpentry tutorial entitled: `The Unix Shell <http://swcarpentry.github.io/shell-novice/>`_

.. note::

	In the "Learn Enough Command Line to be Dangerous..." tutorial, there are two nice boxes describing the `"magic of computers" <https://www.learnenough.com/command-line-tutorial#aside-computer_magic>`_ and `"technical sophistication" <https://www.learnenough.com/command-line-tutorial#aside-technical_sophistication>`_. READ THEM.

[OPTIONAL] A few more Linux shell tutorials that I have found useful are:

* `Learn Enough Command Line to be Dangerous <https://www.learnenough.com/command-line-tutorial>`_
* `Linux Tutorial from Ryan's Tutorials <https://ryanstutorials.net/linuxtutorial/>`_
* `Unix Tutorial for Beginners <http://www.ee.surrey.ac.uk/Teaching/Unix/>`_



Downloads
=========
	
* `Downloads_shell.tar.gz <https://drive.google.com/file/d/1lmYcZTH0lhnbR9YSI_XZR3Gh3RmH0Kvv/view?usp=sharing>`_
* `unix command line cheat sheet <https://www.cheatography.com/davechild/cheat-sheets/linux-command-line/pdf/>`_ (from Dave Child at Cheatography)

- `SCREENCAST: How to extract a tar.gz file in Windows <https://youtu.be/fTBUehkv7EQ>`_ (3:42)

Activities
================================

We will use the presentation slides (in the Downloads) to guide our discussion and hands-on 
exercises to learn the basics of using the bash shell.

What is the bash shell?
-----------------------

- `SCREENCAST: Intro to bash shell <https://youtu.be/d7SPECZCfo4>`_ (6:12)

An example from a research project
----------------------------------

- `SCREENCAST: The CELLDEX project <https://youtu.be/qIuCzJxXEro>`_ (5:17)

File management
--------------------------------

Understanding how the file system is laid out and to do things
like navigating the folder tree, name files, copy/move/delete 
files and directories.

- `SCREENCAST: File management <https://youtu.be/KIuKXDj5CdU>`_ (21:16)


Combining commands to explore and manipulate files
--------------------------------------------------

Use pipes, redirection and filters to accomplish file management tasks by combining multiple shell commands

- `SCREENCAST: Combine shell commands to do useful things <https://youtu.be/jGTMmMGErXg>`_ (10:09)


A few more useful bash commands
--------------------------------------------------

Learn how to use bash to edit files, search files, grab data from websites. Also, where to go to learn more and solutions to the challenges.

- `SCREENCAST: Some additional useful bash commands <https://youtu.be/7R4wEsbVi4M>`_ (15:48)

[OPTIONAL] Intro to Shell for Data Science course at DataCamp
-------------------------------------------------------------

If you're using DataCamp for the Classroom in my class, you also have access to the following course:

* `Intro to Shell for Data Science <https://www.datacamp.com/courses/introduction-to-shell-for-data-science>`_

Sections 1-3 cover very similar ground as done in my screencasts. Subsequent sections go a bit further and
get into shell variables and basic shell scripting. It's interactive and an efficient intro the bash shell.


Explore (OPTIONAL)
==================

* `explainshell.com <https://explainshell.com/>`_ - cool site that explains the pieces of any shell command you want
* `File Not Found <https://www.theverge.com/22684730/students-file-folder-directory-structure-education-gen-z>`_ - a popular article about why younger people may be struggling with the notion of a file and directory structure
* `Bash Guide for Beginners <http://tldp.org/LDP/Bash-Beginners-Guide/html/Bash-Beginners-Guide.html>`_ - tries to fill learning gap
* `How to install and use the bash shell with Windows 10 <https://www.howtogeek.com/249966/how-to-install-and-use-the-linux-bash-shell-on-windows-10/>`_ - a surprising development
* `Anatomy for first year computing and IT students <https://blog.ouseful.info/2016/03/16/anatomy-for-first-year-computing-and-it-students/>`_ - learn how stuff works by exploring its innards