Mark checkpointed re-runs in parallel dictionary allowing bcbio-vm to skip creating docker containers. High level target function to allow running all of bcbio inside of a container
Improve interaction of template creation command with S3 -- download and organize resources directly linking to S3 for running
Provide a tools_off option to force using bwa aln approach. Thanks to @JiantaoShi
Pre-filter BED files to remove non-increasing regions (same start/end or end less than start)
Document bcbio-vm AWS integration, including setting up and running analyses
import pybedtools only when it's used

it does something on initialization that takes ~2.5s, which makes
bcbio_vm.py noticably slow
Merge pull request #660 from jwm/import_pybedtools_on_demand

Import pybedtools only when it's used
Cleanly skip snpEff annotation if not defined in input file for other organisms. Thanks to George Marnellos
Enable automated download of pre-prepared data indexes. Allows bootstrapping runs on minimal AWS machines
Explicitly require click installation to avoid errors from chanjo. Fixes #661
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