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
Remove comments.
RSEM unit test cleans up after itself.
Cloud documentation fixes: support for hg19 (thanks to Yuri) and details on re-creating elasticluster config (chapmanb/bcbio-nextgen-vm#36
VarDict switched to using var2vcf_paire.pl and filter out non-Somatic variants
Provide better defaults for single machine starting docs on AWS
Removed deprecated flags, flags whose purpose had changed
Merge pull request #671 from mjafin/vardict

Vardict syntax updates
joint calling: only upload combined joint calls to final group directory to avoid redundant copies. Correctly assign original single sample calls to individual samples
Fixes for inclusion of GATK jars inside Docker contains when running distributed.
v0.8.4 release
Switch to seaborn as matplotlib wrapper, from the deprecated prettyplotlib