Initial work towards fixing VarScan's VCF output

This covers most of the use cases, although VarScan also produces
invalid REF records (e.g. CAA/A) which aren't handled yet.

Most of the contribution is by Sean Davis, who graciously agreed to
provide it under a MIT license.

This is needed to handle issue #134.
Include mutect and varscan in default system configuration file
Merge pull request #137 from lbeltrame/fix-varscan-output

Initial work towards fixing VarScan's VCF output
Update main entry point to remove deprecated messaging inputs and generalize to new infrastructure. Prepare for moving into module to allow calling from REST API as well as main launch script.
Initial working implementation of bcbio_nextgen standalone REST server to run analysis pipelines
Work on speed improvements for selecting non-analyzed and no-chromosome regions from large BAM inputs files during bamprep stage
Correctly name combined gemini population VCF file. Thanks to @lbeltrame. Fixes #139
Skip "unknown" variants when doing somatic calls with VarScan

VarScan produces broken REF fields when processing "Unknown" records,
which are loci with complex rearrangements (e.g. gain in normal, loss in
tumor). Attempts to workaround the issues have just uncovered more
problems, so for now the solution is to skip these variants.

Once VarScan is fixed, the hacks will be dropped.

This handles issue #134.
Documentation on pipeline processing outputs. #140
Merge pull request #141 from lbeltrame/varscan-skip-unknown

Skip "unknown" variants when doing somatic calls with VarScan
Provide workaround for FreeBayes output containing multiple duplicate alleles
Only require java 1.7 for workflows with variant calling. RNA-seq workflows can use lower version.
Default log timestamps to local time instead of UTC. #140. Uses mitsuhiko/logbook#74
Provide better log messaging for expected VQSR failures, avoiding confusing tracebacks in log file. #140
Avoid loading filtered variants into gemini database for recent gemini versions
Provide todo of current pipeline goals and requested features. Fixes #142
Fix for empty read names with Tophat 2.0.9

Just skips them for now, it seems like a rare occurance.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Avoid VCF preparation steps during ensemble calling to speed up evaluation
Better error message when a non-local IP address cannot be resolved.