Upgrade GLPK to 4.52.

In addition, make tests separately for easier inspection.
Updates to Scalapack formula

- always run tests
- make openblas optional instead of recommended.
New formula for IPOPT.
htslib 0.2.0-rc3: New formula

Used by samtools 0.2.0-rc3
samtools 0.2.0-rc3: --devel

Add --devel. Uses libhts.
igv 2.3.23
armadillo 3.920.2

Closes #418
Revert unintentional regression of samtools

Revert commit 4bf16eb80cd9e09a05a3c69b07c6a1848c1e7e2e
armadillo 3.920.2
armadillo 3.920.2

Closes #418
octave: patch unordered_map bug in configure

Patch to configure, due to a bug in configure.ac, where the ability to
use std::unordered_map as opposed to std::tr1::unordered map was
incorrectly tested, breaking the build on OS X 10.9.

Closes #414
octave: Incorporate upstream patch for std::unordered_map detection.

Follow-up #414.
New formula for CppAD.
tophat: Fails to build with clang

segment_juncs.cpp:50:17: error: expected namespace name
using namespace __gnu_cxx;

Closes #443
root 5.34.11

ROOT: Update to 5.34.11 and add HEAD for 10.9 support

This commit bumps ROOT to version 5.34.11.

It also adds a HEAD URL/branch for additional patches to the current
ROOT release.  The HEAD branch points to the *official* ROOT GitHub
mirror instead of the CERN git server simply because the CERN git server
is primarily for internal use.  While HEAD support is not strictly
necessary for 10.9, adding HEAD will allow users access to more 10.9
patches (since support is still incomplete) before the next ROOT
release.

Closes #421
edena 3.131028
ABySS-Explorer 1.3.4: New formula

ABySS-Explorer is an interactive Java application that employs a novel
graph-based representation to display a sequence assembly and
associated meta data. The tool was designed with the ABySS sequence
assembler in mind and was motivated by the need to examine assembly
structure, in particular contig connectivity and supporting paired-end
read relationships.
htqc 0.90.2: New formula

A toolkit including statistics tool for illumina high-throughput
sequencing data, and filtration tools for sequence quality, length,
tail quality, etc..
kraken 0.10.0-beta: New formula

Kraken is a system for assigning taxonomic labels to short DNA
sequences, usually obtained through metagenomic studies. Previous
attempts to accomplish this task have often used sequence alignment or
machine learning techniques that were quite slow, leading to the
development of less sensitive but much faster abundance estimation
programs. Kraken aims to achieve high sensitivity and high speed by
utilizing exact alignments of k-mers and a novel classification
algorithm.

In its fastest mode of operation, for a simulated metagenome of 100 bp
reads, Kraken processed nearly 4 million reads per minute on a single
core, over 850 times faster than Megablast and over 10 times faster
than the abundance estimation program MetaPhlAn. Kraken's accuracy is
comparable with Megablast, with slightly lower sensitivity and very
high precision.

Kraken is written in C++ and Perl, and is designed for use with the
Linux operating system.
ucsc-genome-browser 291

Closes #445
Trans-ABySS 1.4.8: New formula

Trans-ABySS is a software pipeline for analyzing ABySS-assembled
contigs from shotgun transcriptome data.