Merge pull request #180 from lpantano/upstream

add qsignature
Install oncofuse.
Update homebrew manifest to avoid using deprecated 'brew which' command. Ensure cmake gets updated as dependency to other tools
Add sickle to ngs pipeline dependencies.
Replace sickle with scythe for default installation.
scythe -> sickle
Move Tophat and Bowtie2 to being a homebrew installation.

This moves us off of Tophat 2.0.9, since it has been fixed
to work with the newest Bowtie2.
Replace tophat with tophat-binary.

This removes the boost dependency, which causes issues.
Add delly structural variant caller with binary install. Enable passing arguments to homebrew builds to enable
Support preparation of SNAP aligner indexes. Clean up S3 download error messages to be less worrisome
Ensure spaces used as terminators when preparing SNAP indexes to avoid extra long chromosome names
Update varscan to latest version. Remove duplicate custom snpEff which is no longer needed with bcbio upgrades. Install snap development version by default
Correct target for SNAP aligner
Include R library dependencies for CNVkit. Enable installs of CRAN targets after Bioconductor due to dependencies
If DEXSeq is not found, don't make the DEXseq reference file.
Merge branch 'master' of github.com:chapmanb/cloudbiolinux
Move to samtools 1.0, support brew version checking on devel versions
Update dbNSFP to 2.6. Fixes #181
Fix retrieval of hg19 information from Broad bundle, which has recently changed file naming. Thanks to Jeff Kittrell
Support Psuedomonas genome build