htslib 0.2.0-rc6
samtools 0.2.0-rc6 devel
htslib: Install version.h
bcftools 0.2.0-rc6: New formula
samtools: Add option --without-bcftools

Closes #550
bcftools: Tidy up the formula
NetCDF: update to 4.3.1.1

- remove patch -- this has been merged upstream
- disable the DAP remote tests.

Closes #719.
igv 2.3.31
celera-assembler 8.1: Fails to build with clang

error: use of undeclared identifier 'use_safe_malloc_instead'

Closes #573
celera-assembler: Add a comment mentioning head

Head doesn't build, because the 'kmer' direction is missing.
tophat 2.0.11
genometools 1.5.1: New formula

Genometools is a genome analysis system that consists of a free
collection of bioinformatics tools (in the realm of genome
informatics) combined into a single binary named gt. It is based
on a C library named “libgenometools” which consists of several modules.

Closes #662
genometools 1.5.2
samtools HEAD: Fix the build
samtools: Use build.with? "dwgsim"

Use build.with? "dwgsim" instead of build.include? 'with-dwgsim'
htslib HEAD: Use git rather than a tar.gz

Use https://github.com/samtools/htslib.git
rather than https://github.com/samtools/htslib/archive/develop.tar.gz
viennarna: style cleanup
wcslib: style cleanup
Batch convert http download urls from Google Code to https

Corresponds to upstream audit changes.
R: use brewed gettext

On clean install, update.packages() was failing with:
In file included from R_systat.c:23:
./foreign.h:33:10: fatal error: 'libintl.h' file not found

Closes #676.