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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 Redundans(Package):
"""Redundans pipeline assists an assembly of heterozygous genomes."""
homepage = "https://github.com/Gabaldonlab/redundans"
url = "https://github.com/Gabaldonlab/redundans/archive/v0.13c.tar.gz"
version('0.13c', '2003fb7c70521f5e430553686fd1a594')
depends_on('python', type=('build', 'run'))
depends_on('py-pyscaf', type=('build', 'run'))
depends_on('py-fastaindex', type=('build', 'run'))
depends_on('py-numpy', type=('build', 'run'))
depends_on('perl', type=('build', 'run'))
depends_on('sspace-standard')
depends_on('bwa')
depends_on('last')
depends_on('gapcloser')
depends_on('parallel')
depends_on('snap-berkeley@1.0beta.18:', type=('build', 'run'))
def install(self, spec, prefix):
sspace_location = join_path(spec['sspace-standard'].prefix,
'SSPACE_Standard_v3.0.pl')
mkdirp(prefix.bin)
filter_file(r'sspacebin = os.path.join(.*)$',
'sspacebin = \'' + sspace_location + '\'',
'redundans.py')
install('redundans.py', prefix.bin)
with working_dir('bin'):
install('fasta2homozygous.py', prefix.bin)
install('fasta2split.py', prefix.bin)
install('fastq2insert_size.py', prefix.bin)
install('fastq2mates.py', prefix.bin)
install('fastq2shuffled.py', prefix.bin)
install('fastq2sspace.py', prefix.bin)
install('filterReads.py', prefix.bin)
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