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.
mumps 4.10.0: New formula

MUMPS is a sequential or parallel solver for symmetric linear systems.

Closes #392
tophat: Fix build failure with clang

segment_juncs.cpp:50:17: error: expected namespace name
tophat_reports.cpp:2787:30: error: variable length array of non-POD
element type 'JunctionSet' (aka 'map<Junction, JunctionStats>')

Closes #450
celera-assembler 8.0