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# Copyright 2013-2019 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 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"
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')
def patch(self):
# update cuda architecture if necessary
if '+cuda' in self.spec:
arch = self.spec.variants['cuda_arch'].value
archflag = ''
if arch[0] != 'none':
archflag = '-arch=%s' % arch[0]
filter_file('-arch compute_13', archflag,
'libhmsbeagle/GPU/kernels/Makefile.am',
string=True)
# point CUDA_LIBS to libcuda.so
filter_file('-L$with_cuda/lib', '-L$with_cuda/lib64/stubs',
'configure.ac', string=True)
def configure_args(self):
args = []
if '+cuda' in self.spec:
args.append('--with-cuda=%s' % spec['cuda'].prefix)
else:
args.append('--without-cuda')
return args
def setup_environment(self, spack_env, run_env):
prefix = self.prefix
run_env.prepend_path('BEAST_LIB', prefix.lib)
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