78 lines
3.2 KiB
Python
78 lines
3.2 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 Delly2(MakefilePackage):
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"""Delly2 is an integrated structural variant prediction method that can
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discover, genotype and visualize deletions, tandem duplications,
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inversions and translocations at single-nucleotide resolution in
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short-read massively parallel sequencing data.."""
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homepage = "https://github.com/dellytools/delly"
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url = "https://github.com/dellytools/delly/archive/refs/tags/v1.1.6.tar.gz"
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git = "https://github.com/dellytools/delly.git"
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maintainers("snehring")
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license("BSD-3-Clause")
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version("1.2.6", sha256="1a71fcc5f2a55649c2104086f3f7163ed58c5868eaf040a25e45c777b0e1abb7")
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version("1.1.8", sha256="f72a1143dc71449fc277fc8b3e337a4d35b2fe736f3693a14b1986efa8da4889")
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version("1.1.6", sha256="08961e9c81431eb486476fa71eea94941ad24ec1970b71e5a7720623a39bfd2a")
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version("0.9.1", tag="v0.9.1", commit="ef1cd626a85cfd1c1b7acfca2b5fd5957f2a05f1")
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version("2017-08-03", commit="e32a9cd55c7e3df5a6ae4a91f31a0deb354529fc", deprecated=True)
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depends_on("cxx", type="build") # generated
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variant("openmp", default=False, description="Build with openmp support")
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depends_on("htslib", type=("build", "link"))
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depends_on(
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"boost@:1.78.0+iostreams+filesystem+system+program_options+date_time",
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when="@:0.9.1",
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type=("build", "link"),
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)
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depends_on(
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"boost+iostreams+filesystem+system+program_options+date_time",
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when="@0.9.1:",
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type=("build", "link"),
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)
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depends_on("bcftools", type="run")
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def edit(self, spec, prefix):
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if self.spec.satisfies("+openmp"):
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env["PARALLEL"] = "1"
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# Only want to build delly source, not submodules. Build fails
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# using provided submodules, succeeds with existing spack recipes.
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if self.spec.satisfies("@2017-08-03"):
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makefile = FileFilter("Makefile")
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makefile.filter("HTSLIBSOURCES =", "#HTSLIBSOURCES")
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makefile.filter("BOOSTSOURCES =", "#BOOSTSOURCES")
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makefile.filter("SEQTK_ROOT ?=", "#SEQTK_ROOT")
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makefile.filter("BOOST_ROOT ?=", "#BOOST_ROOT")
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makefile.filter("cd src", "# cd src")
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makefile.filter(".htslib ", "")
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makefile.filter(".bcftools ", "")
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makefile.filter(".boost ", "")
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makefile.filter(".htslib:", "# .htslib:")
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makefile.filter(".bcftools:", "# .bcftools:")
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makefile.filter(".boost:", "# .boost:")
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else:
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env["EBROOTHTSLIB"] = self.spec["htslib"].prefix
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if self.spec.satisfies("@0.9.1"):
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filter_file(
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"BUILT_PROGRAMS =.*$", "BUILT_PROGRAMS = src/delly src/dpe", "Makefile"
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)
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filter_file("${SUBMODULES}", "", "Makefile", string=True)
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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with working_dir("src"):
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install("delly", prefix.bin)
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if self.spec.satisfies("@0.9.1") or self.spec.satisfies("@2017-08-03"):
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install("dpe", prefix.bin)
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if self.spec.satisfies("@2017-08-03"):
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install("cov", prefix.bin)
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