Merge branch 'master' of github.com:denis-yuen/seqware

Conflicts:
	.gitignore
Clean vagrant file
Adding some dummy files and and updated Vagrant file. Still have more SeqWare setup tasks to do in the startup script.
Adding a README
Added a script that will be useful for staging the launch of an instance by collecting various files and params from the user.
Just adding the actual call to launch Vagrant
Notes
Just moving file
Was missing git
Redirect to log file
Just renaming script
Working on vagrant launcher
Forgot to install Maven
Set maven memory settings for seqware user
Merge branch 'develop' of https://github.com/SeqWare/seqware into develop
Working on a script to setup ephemeral disks and add to HDFS, added a settings file for use with testing
Updates to the core scripts
Compatibility with other users and make aws name more descriptive
Necessary to run integration tests
Test