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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 Gcta(CMakePackage):
"""GCTA (Genome-wide Complex Trait Analysis) was originally designed to
estimate the proportion of phenotypic variance explained by all genome-wide
SNPs for complex traits (the GREML method), and has subsequently extended
for many other analyses to better understand the genetic architecture of
complex traits. GCTA currently supports the following analyses."""
homepage = "https://github.com/jianyangqt/gcta"
url = "https://github.com/jianyangqt/gcta/archive/refs/tags/v1.91.2.tar.gz"
git = "https://github.com/jianyangqt/gcta.git"
maintainers("snehring")
version("1.94.0beta", commit="746e3975ddb463fc7bd15b03c6cc64b023eca497", submodules=True)
version("1.91.2", sha256="0609d0fba856599a2acc66adefe87725304117acc226360ec2aabf8a0ac64e85")
conflicts("target=aarch64:", when="@:1.91.2", msg="aarch64 support added in 1.94.0")
depends_on("cmake@3.1:", type="build")
depends_on("intel-mkl@2017:", when="target=x86_64:")
depends_on("openblas", when="target=aarch64:")
depends_on("eigen@3.3.1", when="@1.91.2")
depends_on("eigen@3.3.7:", when="@1.94.0beta:")
depends_on("boost@1.79:", when="@1.94.0beta:")
depends_on("zlib-api")
depends_on("sqlite@3.3.1:", when="@1.94.0beta:")
depends_on("zstd@1.4.4:", when="@1.94.0beta:")
depends_on("spectra", when="@1.94.0beta:")
depends_on("gsl", when="@1.94.0beta:")
def patch(self):
# allow us to specify the locations with cmake_args
strings = [
'SET(EIGEN3_INCLUDE_DIR "$ENV{EIGEN3_INCLUDE_DIR}")',
'SET(SPECTRA_LIB "$ENV{SPECTRA_LIB}")',
'SET(BOOST_LIB "$ENV{BOOST_LIB}")',
'SET(OPENBLAS "$ENV{OPENBLAS}")',
'SET(MKLROOT "$ENV{MKLROOT}")',
]
for s in strings:
filter_file(s, "", "CMakeLists.txt", string=True)
def cmake_args(self):
eigen = self.spec["eigen"].prefix.include
args = [self.define("EIGEN3_INCLUDE_DIR", eigen)]
if self.spec.satisfies("@1.94.0beta:"):
spectra = self.spec["spectra"].prefix.include
boost = self.spec["boost"].prefix.include
deps = [self.define("SPECTRA_LIB", spectra), self.define("BOOST_LIB", boost)]
args.extend(deps)
if self.spec.satisfies("target=x86_64:"):
mkl = self.spec["intel-mkl"].prefix
args.append(self.define("MKLROOT", mkl))
elif self.spec.satisfies("target=aarch64:"):
openblas = self.spec["openblas"].prefix
args.append(self.define("OPENBLAS", openblas))
return args
def install(self, spec, prefix):
mkdirp(prefix.bin)
with working_dir(self.build_directory):
install("gcta64", join_path(prefix.bin, "gcta64"))
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