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# Copyright 2013-2018 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 *
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('2017-08-03', commit='e32a9cd55c7e3df5a6ae4a91f31a0deb354529fc')
depends_on('htslib')
depends_on('boost')
depends_on('bcftools')
def edit(self, spec, prefix):
# Only want to build delly source, not submodules. Build fails
# using provided submodules, succeeds with existing spack recipes.
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:')
def install(self, spec, prefix):
mkdirp(prefix.bin)
with working_dir('src'):
install('delly', prefix.bin)
install('dpe', prefix.bin)
install('cov', prefix.bin)
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