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.
Add switches to x11 and Tcl/Tk

Two switches are added to allow users turn off non-crucial components, namely x11 and Tcl/Tk.

Closes #729.
openni: create and install pkg-config file

Closes #728.
R: fix args for configure

`--without-x` is missing from #133a72a and therefore configure
will not really disable x11.

Closes #730.
R: use RStudio CDN as primary download url
nco 4.4.2

Depends on newer texinfo.

Closes #725.
bedops: improve build process

Fixed optimization flags, removed unused links to libxml2 and
OpenGL libraries, other fixes

Closes #726.
MLPACK: new formula.

MLPACK is a library of machine learning algothms,
see http://mlpack.org for further information.

Closes #715.
Z3 theorem prover: new formula

Closes #289.