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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.package import *
from spack.pkg.builtin.boost import Boost
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"
git = "https://github.com/dellytools/delly.git"
version('0.9.1', tag='v0.9.1')
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', type=('build', 'link'))
# 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)
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
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)
install('dpe', prefix.bin)
if self.spec.satisfies('@2017-08-03'):
install('cov', prefix.bin)
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