66 lines
2.2 KiB
Python
66 lines
2.2 KiB
Python
# Copyright Spack Project Developers. See COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack.package import *
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class Cnvnator(MakefilePackage):
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"""A tool for CNV discovery and genotyping
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from depth-of-coverage by mapped reads."""
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homepage = "https://github.com/abyzovlab/CNVnator"
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url = "https://github.com/abyzovlab/CNVnator/archive/v0.3.3.tar.gz"
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version("0.3.3", sha256="58c5acf61f9a1e5febf546c196f8917a5e084b729e5c4cfd3eba83471b3fe5c1")
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depends_on("cxx", type="build") # generated
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depends_on("samtools@:1.13")
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depends_on("htslib")
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depends_on("root")
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depends_on("bzip2")
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depends_on("curl")
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depends_on("xz")
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depends_on("zlib-api")
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depends_on("libdeflate")
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depends_on("openssl")
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def edit(self, spec, prefix):
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makefile = FileFilter("Makefile")
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# Replace -fopenmp with self.compiler.openmp_flag
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makefile.filter("-fopenmp", self.compiler.openmp_flag)
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# Replace CXX with CXXFLAGS
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makefile.filter(
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"CXX.*=.*",
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r"CXXFLAGS = -DCNVNATOR_VERSION=\"$(VERSION)\""
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" $(OMPFLAGS)"
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" {0}".format(self.compiler.cxx11_flag),
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)
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makefile.filter("$(CXX)", "$(CXX) $(CXXFLAGS)", string=True)
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# Replace -I$(SAMDIR) with -I$(SAMINC)
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makefile.filter("-I$(SAMDIR)", "-I$(SAMINC)", string=True)
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# Link more libs
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ldflags = [
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spec["zlib-api"].libs.ld_flags,
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spec["bzip2"].libs.ld_flags,
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spec["curl"].libs.ld_flags,
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spec["xz"].libs.ld_flags,
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spec["libdeflate"].libs.ld_flags,
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spec["openssl"].libs.ld_flags,
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]
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makefile.filter("^override LIBS.*", "override LIBS += {0}".format(" ".join(ldflags)))
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def build(self, spec, prefix):
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make(
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"ROOTSYS={0}".format(spec["root"].prefix),
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"SAMINC={0}".format(spec["samtools"].prefix.include),
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"SAMDIR={0}".format(spec["samtools"].prefix.lib),
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"HTSDIR={0}".format(spec["htslib"].prefix.lib),
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)
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def install(self, spec, prefix):
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mkdir(prefix.bin)
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install("cnvnator", prefix.bin)
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