desc "RAxML Next Generation: faster, easier-to-use and more flexible"

homepage "https://cme.h-its.org/exelixis/web/software/raxml/"

url "https://github.com/amkozlov/raxml-ng.git",

tag: "1.2.2",

revision: "805318cef87bd5d67064efa299b5d1cf948367fd"

license "AGPL-3.0-or-later"

bottle do

sha256 cellar: :any, arm64_sequoia: "4f7e500c5a3615a4c814bf38bd8720a745c4155827910f4cd5638113e129d2c6"

sha256 cellar: :any, arm64_sonoma: "bd6bd94ccee20b21d5c9146a8bc4a484c261a11586224ec4303a2d269590b32f"

sha256 cellar: :any, arm64_ventura: "6fcf4ec42def10fd485108f16f3d9c03f59f06ff72b663e469d7985332b99222"

sha256 cellar: :any, arm64_monterey: "a2e435fabdb95292270d576aa6fd6dceda14ad722cd12ccb916371b8aa01e0a4"

sha256 cellar: :any, sonoma: "63100f2fe0b660b831fcb16cc08b299bf62a978d4c97949d87d5e09716b4670d"

sha256 cellar: :any, ventura: "456c5f39dacdc8ce957c17d67f53410977c8217bc98ca45ba97c1df187442aa9"

sha256 cellar: :any, monterey: "7bbd86f8a89f92287d21cab56e055333a5c5ec90e955b76f78d3c8a36cb9dda4"

sha256 cellar: :any_skip_relocation, arm64_linux: "9aa9f1417b9bf4ed64b5e690d2a6901d5c181cc9fd8e641589301b8118d2ab1b"

sha256 cellar: :any_skip_relocation, x86_64_linux: "53e258a6db4cb2d05aa6013741ac3c2345a9d92da103a23d34dda647b8e8d532"

end

depends_on "bison" => :build # fix syntax error with `parse_utree.y`

depends_on "cmake" => :build

depends_on "gmp"

uses_from_macos "flex" => :build

on_linux do

depends_on "open-mpi"

end

resource "homebrew-example" do

url "https://cme.h-its.org/exelixis/resource/download/hands-on/dna.phy"

sha256 "c2adc42823313831b97af76b3b1503b84573f10d9d0d563be5815cde0effe0c2"

end

def install

args = std_cmake_args + ["-DUSE_GMP=ON"]

system "cmake", "-S", ".", "-B", "build", *args

system "cmake", "--build", "build"

system "cmake", "--install", "build"

# Upstream doesn't support building MPI variant on macOS.

# The build ignores USE_MPI=ON and forces ENABLE_MPI=OFF.

# This causes necessary flags like -D_RAXML_MPI to not get set.

return if OS.mac?

system "cmake", "-S", ".", "-B", "build_mpi", *args, "-DUSE_MPI=ON"

system "cmake", "--build", "build_mpi"

system "cmake", "--install", "build_mpi"

end

test do

testpath.install resource("homebrew-example")

system bin/"raxml-ng", "--msa", "dna.phy", "--start", "--model", "GTR"

end