59 lines
2.0 KiB
Python
59 lines
2.0 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 Shapeit4(MakefilePackage):
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"""SHAPEIT4 is a fast and accurate method for estimation of haplotypes
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(aka phasing) for SNP array and high coverage sequencing data."""
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homepage = "https://odelaneau.github.io/shapeit4/"
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url = "https://github.com/odelaneau/shapeit4/archive/v4.1.3.tar.gz"
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license("MIT")
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version("4.2.2", sha256="9f109e307b5cc22ab68e7bf77de2429a9bbb2212d66303386e6a3dd81a5bc556")
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version("4.1.3", sha256="d209731277b00bca1e3478b7e0a0cbe40fbe23826c3d640ad12e0dd6033cbbb8")
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depends_on("cxx", type="build") # generated
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maintainers("ilbiondo")
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depends_on("htslib")
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depends_on("boost+exception+container+iostreams+program_options")
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depends_on("bzip2")
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depends_on("xz")
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def edit(self, spec, prefix):
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makefile = FileFilter("makefile")
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makefile.filter("CXX=.*", "CXX = c++")
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makefile.filter("CXXFLAG=.*", "CXXFLAG = -O3")
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makefile.filter("LDFLAG=.*", "LDFLAG = -O3")
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makefile.filter("HTSLIB_INC=.*", "HTSLIB_INC = " + self.spec["htslib"].prefix.include)
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makefile.filter(
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"HTSLIB_LIB=.*", "HTSLIB_LIB = " + self.spec["htslib"].prefix.lib + "/libhts.so"
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)
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makefile.filter("BOOST_INC=.*", "BOOST_INC = " + self.spec["boost"].prefix.include)
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makefile.filter(
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"BOOST_LIB_IO=.*",
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"BOOST_LIB_IO = " + self.spec["boost"].prefix.lib + "/libboost_iostreams.so",
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)
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makefile.filter(
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"BOOST_LIB_PO=.*",
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"BOOST_LIB_PO = " + self.spec["boost"].prefix.lib + "/libboost_program_options.so",
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)
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def install(self, spec, prefix):
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install_tree("bin", prefix.bin)
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install_tree("test", join_path(self.prefix, "test"))
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install_tree("docs", join_path(self.prefix, "docs"))
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install_tree("maps", join_path(self.prefix, "maps"))
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