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# Copyright 2013-2022 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 import *
from spack.pkg.builtin.boost import Boost
class Denovogear(CMakePackage):
"""DeNovoGear is a software package to detect de novo mutations using
next-generation sequencing data. It supports the analysis of many
differential experimental designs and uses advanced statistical models
to reduce the false positve rate."""
homepage = "https://github.com/denovogear/denovogear"
url = "https://github.com/denovogear/denovogear/archive/v1.1.1.tar.gz"
version('1.1.1', sha256='799fe99193e9cf12320893cf020a3251022f60a49de8677a1c5a18c578fe4be2')
version('1.1.0', sha256='f818f80cd67183294c8aae312cad8311e6a9abede1f687567bb079d29f79c005')
depends_on('cmake@3.1:', type=('build'))
depends_on('boost@1.47:1.60', type=('build'))
# TODO: replace this with an explicit list of components of Boost,
# for instance depends_on('boost +filesystem')
# See https://github.com/spack/spack/pull/22303 for reference
depends_on(Boost.with_default_variants, type=('build'))
depends_on('htslib@1.2:', type=('build'))
depends_on('eigen', type=('build'))
depends_on('zlib', type=('link'))
patch('stream-open.patch', when='@:1.1.1')
# fix: ordered comparison between pointer and zero.
patch('newmat6.cpp.patch')
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