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delly2: add v1.1.6 (#34411)

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snehring 2022-12-12 04:31:26 -06:00 committed by GitHub
parent 62da76cb5d
commit 47628521b9
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1 changed files with 19 additions and 8 deletions
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27
var/spack/repos/builtin/packages/delly2/package.py
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@ -4,7 +4,6 @@
# SPDX-License-Identifier: (Apache-2.0 OR MIT) # SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import * from spack.package import *
from spack.pkg.builtin.boost import Boost
class Delly2(MakefilePackage): class Delly2(MakefilePackage):
@ -14,19 +13,27 @@ class Delly2(MakefilePackage):
short-read massively parallel sequencing data..""" short-read massively parallel sequencing data.."""
homepage = "https://github.com/dellytools/delly" 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" git = "https://github.com/dellytools/delly.git"
maintainers = ["snehring"]
version("1.1.6", sha256="08961e9c81431eb486476fa71eea94941ad24ec1970b71e5a7720623a39bfd2a")
version("0.9.1", tag="v0.9.1") version("0.9.1", tag="v0.9.1")
version("2017-08-03", commit="e32a9cd55c7e3df5a6ae4a91f31a0deb354529fc", deprecated=True) version("2017-08-03", commit="e32a9cd55c7e3df5a6ae4a91f31a0deb354529fc", deprecated=True)
variant("openmp", default=False, description="Build with openmp support") variant("openmp", default=False, description="Build with openmp support")
depends_on("htslib", type=("build", "link")) depends_on("htslib", type=("build", "link"))
depends_on("boost", type=("build", "link")) depends_on(
# TODO: replace this with an explicit list of components of Boost, "boost@:1.78.0+iostreams+filesystem+system+program_options+date_time",
# for instance depends_on('boost +filesystem') when="@:0.9.1",
# See https://github.com/spack/spack/pull/22303 for reference type=("build", "link"),
depends_on(Boost.with_default_variants) )
depends_on(
"boost+iostreams+filesystem+system+program_options+date_time",
when="@0.9.1:",
type=("build", "link"),
)
depends_on("bcftools", type="run") depends_on("bcftools", type="run")
def edit(self, spec, prefix): def edit(self, spec, prefix):
@ -49,13 +56,17 @@ def edit(self, spec, prefix):
makefile.filter(".boost:", "# .boost:") makefile.filter(".boost:", "# .boost:")
else: else:
env["EBROOTHTSLIB"] = self.spec["htslib"].prefix env["EBROOTHTSLIB"] = self.spec["htslib"].prefix
filter_file("BUILT_PROGRAMS =.*$", "BUILT_PROGRAMS = src/delly src/dpe", "Makefile") if self.spec.satisfies("@0.9.1"):
filter_file(
"BUILT_PROGRAMS =.*$", "BUILT_PROGRAMS = src/delly src/dpe", "Makefile"
)
filter_file("${SUBMODULES}", "", "Makefile", string=True) filter_file("${SUBMODULES}", "", "Makefile", string=True)
def install(self, spec, prefix): def install(self, spec, prefix):
mkdirp(prefix.bin) mkdirp(prefix.bin)
with working_dir("src"): with working_dir("src"):
install("delly", prefix.bin) install("delly", prefix.bin)
install("dpe", 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"): if self.spec.satisfies("@2017-08-03"):
install("cov", prefix.bin) install("cov", prefix.bin)