46 lines
1.7 KiB
Python
46 lines
1.7 KiB
Python
# Copyright 2013-2020 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)
|