biocgal 0.9.6-beta: New formula

The name CGAL conflicts with
Computational Geometry Algorithms Library
reapr 1.0.16: New formula

REAPR is a tool that evaluates the accuracy of a genome assembly using
mapped paired end reads, without the use of a reference genome for
comparison.
maker 2.31: Add optional dependencies for MAKER-P

infernal and trnascan
ensembl-tools 75: New formula

Tools include:
variant_effect_predictor
assembly_converter
id_history_converter
region_reporter
gmcloser 1.2: New formula
opencv 2.4.8.2

Set proper paths for python and openni. Build requires ant.

Closes #622. Closes #681.
opencv: move openni option inside block
bamutil 1.0.11
allpaths-lg: fix url

Add fails_with for GCC >=4.7 requirement.

Closes #361.
analysis 0.8.4

Closes #718.
wcstools 3.8.7 (new formula)

Closes #717.
Update R formula to 3.03

R version 3.0.3 (Warm Puppy) has been released on 2014-03-06.
See http://cran.r-project.org/src/base/NEWS.html

Closes #720.
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