pbsuite 14.7.14
sspace-longread 1-1

SSPACE-LongRead is a stand-alone program for scaffolding pre-assembled contigs
using long reads (e.g. PacBio RS reads). Using the long read information,
contigs (or scaffolds) are placed in the right order and orientation in
so-called super-scaffolds.
platanus: use gcc opt_lib
opencv: add gstreamer, quicktime options

Recommend OpenEXR for interoperability.

Closes #951.
corset 1.02 (new formula)

Closes #1138.
cerulean 0.1: New formula

Cerulean extends contigs assembled using short read datasets like Illumina
paired-end reads using long reads like PacBio RS long reads.
update vips,rb to 7.40.6

- fix similarity rotate+scale
- fix 16-bit PNG save
- fix vipsthumbnail on many-core systems

Closes #1140.
vips: style cleanup
abyss-explorer: add doi, tag
ucsc-genome-browser 304
lumpy-sv: update to 0.2.7, remove Perl dependency

Closes #1144.
Move OpenFST, OpenGRM-ngram, and OpenGRM-thrax from core

As per the discussion in
https://github.com/Homebrew/homebrew/pull/31888, the maintainers feel
that homebrew-science is the right place for OpenFST and OpenGRM. I have
moved two homebrew formulae here (openfst and opengrm-ngram) as well as
a new one, opengrm-thrax, which also depends on OpenFST.

OpenGRM-thrax is a tool for compiling morphological analyzers and
context-sensitive rewrite rules into OpenFST automata.

Closes #1146.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>
primer3: add primer3_config

Closes #1143.
adam 0.13.0 (new formula)

ADAM is a JVM based system for processing genomic data. ADAM runs
on the Apache Spark computing framework and can run both locally
and distributed across a cluster.

Closes #1142.
root 5.34.20

Closes #1155.
lp_solve: fix audit warning

Use NumpyHasHeaders over LanguageModuleDependency.
graph-tool: use Python module deps

Closes #1134.
openblas 0.2.11
lp_solve: fix typo
viennarna 2.1.8