Initial commit
Added an initial minimal Vagrantfile
Added a basic Vagrantfile for configuring a few machines and pushing in basic ansible using a dummy playbook so we actually get an inventory
The magic command to run ansible on the Vagrant generated inventory
Added the Java role
Added the database role
Added common role info, this generates the hosts file and sets the hostname
Whoa - forgot to add the global playbook
Pipeline role stuff, such as Python, R, and so on.
Added some SGE master stuff
Initial Seqware stuff -- incomplete and not yet used
Changed notes to a deploy script
Fixed the deploy script
Slightly filled out README.md
Added a good amount of work on deploying the web app
Fixed the Java install to set the alternative. This should avoid Maven pulling in a different version and getting conflicted about class file versions.
Use the git module rather than the shell module
Add the pipeline role to the workers
Fixed the git handling that I fscked up last time. Also added it to the web app, where I thought I had last time, which is why it seemed to work OK
Full build process for the main aligners and inclusion in the pipeline deployment