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Cheat Sheet: Simple Authentication in Rails 5 with `has_secure_password`

The goal of this cheatsheet is to make it easy to add hand-rolled authentication to any rails app in a series of layers.

First the simplest/core layers, then optional layers depending on which features/functionality you want.

`Specs`
AUTHOR	Ira Herman
LANGUAGE/STACK	Ruby on Rails Version 4 or 5

#Simple Authentication with Bcrypt

This tutorial is for adding authentication to a vanilla Ruby on Rails app using Bcrypt and has_secure_password.

The steps below are based on Ryan Bates's approach from Railscast #250 Authentication from Scratch (revised).

You can see the final source code here: repo. I began with a stock rails app using rails new gif_vault

##Steps

SAM and BAM filtering one-liners

Please comment or extend with additional/faster/better solutions.

BWA mapping (using piping for minimal disk I/O)

	// answer to http://weibo.com/1915548291/z2UtyzuvQ
	// see also http://www.cnblogs.com/baiyanhuang/archive/2012/11/11/2764914.html

	#include <boost/bind.hpp>
	#include <boost/function.hpp>
	#include <boost/noncopyable.hpp>
	#include <boost/ptr_container/ptr_vector.hpp>

	#include <fstream>
	#include <iostream>

	sudo apt-get install python-software-properties
	sudo add-apt-repository ppa:ubuntu-toolchain-r/test
	sudo apt-get update
	sudo apt-get install gcc-4.9
	sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 50
	sudo apt-get install g++-4.9
	sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.9 50

	"""
	align reads with bwa mem
	remove duplicates with samblaster
	call variants with freebayes
	"""
	import sys
	import os.path as op
	import os

	def base(fq):