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# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class Mrbayes(AutotoolsPackage):
"""MrBayes is a program for Bayesian inference and model choice across a
wide range of phylogenetic and evolutionary models. MrBayes uses Markov
chain Monte Carlo (MCMC) methods to estimate the posterior distribution
of model parameters."""
homepage = "http://mrbayes.sourceforge.net"
url = "https://github.com/NBISweden/MrBayes/releases/download/v3.2.7a/mrbayes-3.2.7a.tar.gz"
license("GPL-3.0-or-later")
version("3.2.7a", sha256="1a4670be84e6b968d59382328294db4c8ceb73e0c19c702265deec6f2177815c")
version("3.2.7", sha256="39d9eb269969b501268d5c27f77687c6eaa2c71ccf15c724e6f330fc405f24b9")
variant("mpi", default=True, description="Enable MPI parallel support")
variant("beagle", default=True, description="Enable BEAGLE library for speed benefits")
variant(
"readline", default=False, description="Enable readline library, not recommended with MPI"
)
depends_on("libbeagle", when="+beagle")
depends_on("mpi", when="+mpi")
depends_on("readline", when="+readline")
def configure_args(self):
args = []
if "~beagle" in self.spec:
args.append("--with-beagle=no")
else:
args.append("--with-beagle=%s" % self.spec["libbeagle"].prefix)
if "+readline" in self.spec:
args.append("--with-readline=yes")
else:
args.append("--with-readline=no")
if "~mpi" in self.spec:
args.append("--with-mpi=no")
else:
args.append("--with-mpi=yes")
return args
def install(self, spec, prefix):
mkdirp(prefix.bin)
with working_dir("src"):
install("mb", prefix.bin)
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