piler 1.0: New formula

PILER is public domain software for analyzing repetitive DNA found in
genome sequences.
repeatscout 1.0.5: New formula

RepeatScout is a tool to discover repetitive substrings in DNA.
recon 1.05: New formula

The RECON package performs de novo identification and classification
of repeat sequence families from genomic sequences.
recon 1.07

The 1.07 version fixes problems with running RECON on 64 bit machines
and supplies a workaround to a division by zero bug.
Tmv-Cpp: New formula.

Closes #544.
Petsc: upgrade to 3.4.4.
quicktree: new download url

Closes #754.
giira 20140221: New formula

GIIRA is a stand-alone java program to predict genes based on RNA-Seq
reads without requiring any a-priori knowledge.
root 5.34.18

Closes #750.
allpaths-lg: fails_with any clang version
Bump fails_with clang versions
kraken 0.10.3-beta
snpeff 3.5e
snpeff: set share dir for downloads

Move snpEff.config to #{share} and keeps jars in #{libexec}, downloads
are extracted into #{share}/data.
giira: fix audit warnings
viennarna: fix audit warnings
mrbayes: fix audit warnings
openimageio: fix audit warnings
h5utils: use checksummed patches
tmv-cpp: use checksummed patches