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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 Libbeagle(AutotoolsPackage, CudaPackage):
"""Beagle performs genotype calling, genotype phasing, imputation of
ungenotyped markers, and identity-by-descent segment detection."""
homepage = "https://github.com/beagle-dev/beagle-lib"
url = "https://github.com/beagle-dev/beagle-lib/archive/v3.1.2.tar.gz"
license("LGPL-3.0-or-later")
version("3.1.2", sha256="dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275")
version(
"2.1.2",
sha256="82ff13f4e7d7bffab6352e4551dfa13afabf82bff54ea5761d1fc1e78341d7de",
url="https://github.com/beagle-dev/beagle-lib/archive/beagle_release_2_1_2.tar.gz",
)
depends_on("autoconf", type="build")
depends_on("automake", type="build")
depends_on("libtool", type="build")
depends_on("m4", type="build")
depends_on("subversion", type="build")
depends_on("pkgconfig", type="build")
depends_on("java", type="build")
depends_on("opencl", when="+opencl")
cuda_arch_values = CudaPackage.cuda_arch_values
variant("opencl", default=False, description="Include OpenCL (GPU) support")
variant(
"cuda_arch",
description="CUDA architecture",
default="none",
values=("none",) + cuda_arch_values,
multi=False,
)
conflicts("cuda_arch=none", when="+cuda", msg="must select a CUDA architecture")
def patch(self):
# update cuda architecture if necessary
if "+cuda" in self.spec:
cuda_arch = self.spec.variants["cuda_arch"].value
archflag = "-arch=compute_{0}".format(cuda_arch)
filter_file(
"-arch compute_13", "", "libhmsbeagle/GPU/kernels/Makefile.am", string=True
)
filter_file(r'(NVCCFLAGS="-O3).*(")', r"\1 {0}\2".format(archflag), "configure.ac")
# point CUDA_LIBS to libcuda.so
filter_file(
"-L$with_cuda/lib", "-L$with_cuda/lib64/stubs", "configure.ac", string=True
)
def autoreconf(self, spec, prefix):
which("bash")("autogen.sh")
def configure_args(self):
args = [
# Since spack will inject architecture flags turn off -march=native
# when building libbeagle.
"--disable-march-native"
]
if "+cuda" in self.spec:
args.append("--with-cuda={0}".format(self.spec["cuda"].prefix))
else:
args.append("--without-cuda")
if "+opencl" in self.spec:
args.append("--with-opencl={0}".format(self.spec["opencl"].prefix))
else:
args.append("--without-opencl")
return args
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