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