Fixes for on-demand genome downloads with no reference data. Update cloud documentation to match no pre-build AMI
Document setting root volume size and NFS sharing on AWS. Support functionality for handling pre-prepared genomes on AWS
Move from plzip to pigz for parallel compression/decompression. Not much practical space improvement with plzip
Move transcriptome-only mapping file to final directory.

This will let us use it to run RSEM later on.
hg19 installation without GRCh37: Only use VEP symlinks if GRCh37 present
Use correct separator for LOFTEE human_ancestor file. Thanks to @drmjc. #468
Set precision for bedtools groupby to handle change in behavior in 2.22.0. Fixes #664
Allow mutect to accept additional parameters

Users can now define additional parameters in the resources section of YAML.
Merge pull request #665 from a113n/patch-1

Allow mutect to accept additional parameters
Support WHAM VCF to BED conversion and bump cnvkit to released version with support for setting R libraries
v0.8.3 release
Enable on demand preparation of STAR indexes. Refactors sample setup and genome download into a processing component so it occurs isolated and with access to multiple CPU/memory
Add transcriptome-mapped BAM to data dictionary.

Access it with dd.get_transcriptome_bam(data).
Enable remote reads to feed into RNA-seq pipelines, removing existance checks when located remotely
Improve parallelization of trimming but splitting out from sample/genome preparation and alignment so it can run single core
Small cleanups to cutadapt usage in setting up parallel run and log messages. Unique naming for organize samples steps in timing logs
Ensure vagrant shell script fails if vagrant not present. Fixes #669
Improve documentation on SLURM thanks to feedback from @kern3020. Document restarting if run into issues during setup
Functions to quantitate gene and isoform expression with RSEM.

With unit tests-- needs some wrapper functions to work with
bcbio and to handle strandedness properly.
Merge branch 'master' of https://github.com/chapmanb/bcbio-nextgen