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# Copyright 2013-2023 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 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"
license("MIT")
version("1.3.6", sha256="6016c1e58fdf34a1f6f77b720dd8e12e13a127f7cbac9c747e47954561b437f5")
version("1.3.5", sha256="7e2635690e916ed85cec36b3263e6e5357413a4f2bf3035362d9749335e8a696")
version(
"1.1.0",
commit="39e5e4bcb801556141f2da36aba1df5c5c60701f",
submodules=True,
deprecated=True,
)
depends_on("cmake", type="build")
depends_on("zlib-api")
# 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-api", 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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