picard-tools 1.111

Closes #807
picard-tools: Add a test
giira: fix url

Newer release removed by upstream.
quast 2.3

Add a DOI.
prodigal: update url, add HEAD

Development moved to GitHub.
oce 0.15

Closes #803.
edirect 1.60
glimmerhmm 3.0.2: New formula

GlimmerHMM
Eukaryotic Gene-Finding System
igv 2.3.32
cufflinks 2.2.0

Builds with latest clang, linked against bottled Boost.
ucsc-genome-browser 297
atpdec 1.7 (new formula)

NOAA POES weather satellite image software decoder.

Closes #799.
snp_sites 1.5.0
bwa 0.7.8
ensembl-tools: fix url
ensembl-tools: update sha1

Catch up with latest changes to release/75 branch.
Add caveat to ammend PERL5LIB with libexec.
lumpy-sv 0.2.0

Also removes GSL dependency and patch, simplifying build.

Closes #812.
radx 20140401
Add contributing guidelines to root.
New formula: Lis 1.4.34

Closes #806.