symlink ansible and elasticluster files when developing
Merge pull request #25 from jwm/setup_py_develop_target_symlinks

Symlink ansible and elasticluster files when developing
Automatically link GATK and MuTect jar files present in a 'jars' directory relative to a configuration stored on S3
Support non-absolute system configuration input file names
Fix mounting of reference directories for test cases -- handle relative reference genome inputs
Provide subcommand to make it easier to edit and update bcbio-nextgen in a docker container during development
Re-run checkpointed functions outside of docker container to save overhead of spinning up on re-checks. Simplify mounting of input directories and avoid remapping internally
Link to template creation command for direct access through bcbio-vm. Pass along AWS keys to docker instances for upload/download
Automate setting bcbio_system file to a target set of cores and memory. Include update as part of AWS bcbio bootstrapping
Move AWS documentation over to bcbio read the docs site
add trailing newlines
move ansible utils, ecluster_config into common module
only import bcbio.pipeline.main when it's needed

along with d40541cc in bcbio-nextgen, this cuts bcbio_vm.py startup time
in half (~5s -> ~2.5s)