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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 Cnvnator(MakefilePackage):
"""A tool for CNV discovery and genotyping
from depth-of-coverage by mapped reads."""
homepage = "https://github.com/abyzovlab/CNVnator"
url = "https://github.com/abyzovlab/CNVnator/archive/v0.3.3.tar.gz"
version("0.3.3", sha256="58c5acf61f9a1e5febf546c196f8917a5e084b729e5c4cfd3eba83471b3fe5c1")
depends_on("samtools@:1.13")
depends_on("htslib")
depends_on("root")
depends_on("bzip2")
depends_on("curl")
depends_on("xz")
depends_on("zlib-api")
depends_on("libdeflate")
depends_on("openssl")
def edit(self, spec, prefix):
makefile = FileFilter("Makefile")
# Replace -fopenmp with self.compiler.openmp_flag
makefile.filter("-fopenmp", self.compiler.openmp_flag)
# Replace CXX with CXXFLAGS
makefile.filter(
"CXX.*=.*",
r"CXXFLAGS = -DCNVNATOR_VERSION=\"$(VERSION)\""
" $(OMPFLAGS)"
" {0}".format(self.compiler.cxx11_flag),
)
makefile.filter("$(CXX)", "$(CXX) $(CXXFLAGS)", string=True)
# Replace -I$(SAMDIR) with -I$(SAMINC)
makefile.filter("-I$(SAMDIR)", "-I$(SAMINC)", string=True)
# Link more libs
ldflags = [
spec["zlib-api"].libs.ld_flags,
spec["bzip2"].libs.ld_flags,
spec["curl"].libs.ld_flags,
spec["xz"].libs.ld_flags,
spec["libdeflate"].libs.ld_flags,
spec["openssl"].libs.ld_flags,
]
makefile.filter("^override LIBS.*", "override LIBS += {0}".format(" ".join(ldflags)))
def build(self, spec, prefix):
make(
"ROOTSYS={0}".format(spec["root"].prefix),
"SAMINC={0}".format(spec["samtools"].prefix.include),
"SAMDIR={0}".format(spec["samtools"].prefix.lib),
"HTSDIR={0}".format(spec["htslib"].prefix.lib),
)
def install(self, spec, prefix):
mkdir(prefix.bin)
install("cnvnator", prefix.bin)
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