This Vagrantfile and chef cookbook are designed for creating the Bioconductor Amazon Machine Image (AMI), but could also be used to provision a virtual machine (Virtualbox or VMware) or a physical machine.
It's designed to work on Ubuntu but could be modified to work on other Linux distributions.
It is typically used with a base StarCluster AMI to which Chef has been added, but you could use it with any AMI or Vagrant Box that has Chef installed.
You'll need Vagrant installed in order to use this.
To use, copy config.yml.example to config.yml and edit config.yml to taste. If you are creating an Amazon AMI you'll need the AWS plugin for Vagrant.
These scripts are designed for creating a machine from scratch. If you want to modify an existing AMI, it is much simpler to follow the instructions here.