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# Copyright 2013-2022 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 Freebayes(MesonPackage):
"""Bayesian haplotype-based genetic polymorphism discovery and
genotyping."""
homepage = "https://github.com/ekg/freebayes"
url = "https://github.com/freebayes/freebayes/releases/download/v1.3.5/freebayes-1.3.5-src.tar.gz"
git = "https://github.com/ekg/freebayes.git"
version('1.3.5', sha256='7e2635690e916ed85cec36b3263e6e5357413a4f2bf3035362d9749335e8a696')
version('1.1.0', commit='39e5e4bcb801556141f2da36aba1df5c5c60701f',
submodules=True, deprecated=True)
depends_on('cmake', type='build')
depends_on('zlib')
# Deps for @1.3.5 and beyond
depends_on('ninja', type='build', when='@1.3.5:')
depends_on('pkgconfig', type='build', when='@1.3.5:')
depends_on('htslib', when='@1.3.5:')
depends_on('zlib', when='@1.3.5:')
depends_on('xz', when='@1.3.5:')
depends_on('parallel', when='@1.3.5:')
depends_on('vcftools', when='@1.3.5:')
depends_on('bc', when='@1.3.5:')
depends_on('samtools', when='@1.3.5:')
parallel = False
@when('@:1.1.0')
def edit(self, spec, prefix):
makefile = FileFilter('Makefile')
b = prefix.bin
makefile.filter('cp bin/freebayes bin/bamleftalign /usr/local/bin/',
'cp bin/freebayes bin/bamleftalign {0}'.format(b))
@when('@:1.1.0')
@run_before('install')
def make_prefix_dot_bin(self):
mkdir(prefix.bin)
@when('@:1.1.0')
def meson(self, spec, prefix):
pass
@when('@:1.1.0')
def build(self, spec, prefix):
make()
@when('@:1.1.0')
def install(self, spec, prefix):
make('install')
@property
def vcflib_builddir(self):
return join_path(self.build_directory, 'vcflib')
@when('@1.3.4:')
def setup_build_environment(self, env):
if self.run_tests:
env.prepend_path('PATH', self.vcflib_builddir)
env.prepend_path('PATH', self.build_directory)
@when('@1.3.4:')
def check(self):
mkdir(self.vcflib_builddir)
with working_dir(self.vcflib_builddir):
cmake('../../vcflib')
make()
with working_dir(self.build_directory):
ninja('test')
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