Bump VarDict to include latest fixes (thanks to @mjafin)
Bug fixes to variant fields 

to suppress Gatk errors
Merge pull request #11 from lpantano/master

add qsignature formula
Deparallelize makefiles on several tools to avoid errors on gcc-4.1. Thanks to Craig Bohrson
Add oncofuse.
Install STARstatic instead of STAR.

This allows STAR to run on more legacy systems.
Add skewer, a fast k-mer based read trimmer.
Cleaner installation code for rna-star.
Update vardict.rb

Bug fixes for correct header fields and amplicon based calling. Produces less output to stderr.
Install binaries of Tophat.

Boost is problematic to build on some machines, so install
binaries for Tophat instead.
Explicitly compile freebayes fsom submodule to avoid compile errors reported on gcc 4.1. Thanks to Craig Bohrson
Move to GATK framework 3.2-2 with fix for -XX java specifications
Update vt and vcflib to latest GitHub versions with fixes for normalization and vcfcat
Update GATK framework to handle non-engine runs like CatVariants
SNAP aligner: build target for current development version
Update vardict.rb to pull bug fixes in vcf headers
Updates for SNAP to default development version; scalpel to 0.2.1 release; vardict to latest GitHub revision with GATK compatible VCF
platypus: update to latest release v0.7.8; chapmanb/bcbio-nextgen#558
Update speedseq and Hall Lab SV tools to latest versions. Avoids issues with recursively cloning speedseq, which we don't need.
Update oncofuse to 1.0.7