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# Copyright 2013-2019 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 HicPro(MakefilePackage):
"""HiC-Pro is a package designed to process Hi-C data,
from raw fastq files (paired-end Illumina data)
to the normalized contact maps"""
homepage = "https://github.com/nservant/HiC-Pro"
url = "https://github.com/nservant/HiC-Pro/archive/v2.10.0.tar.gz"
version('2.10.0', sha256='df181ea5c57247caf6b25fd15dfbb03df597ff8c4f57599d88607648bb61f1b7')
depends_on('bowtie2')
depends_on('samtools')
depends_on('python+ucs4@2.7:2.8')
depends_on('r')
depends_on('py-numpy', type=('build', 'run'))
depends_on('py-scipy', type=('build', 'run'))
depends_on('py-pysam', type=('build', 'run'))
depends_on('py-bx-python', type=('build', 'run'))
depends_on('r-rcolorbrewer', type=('build', 'run'))
depends_on('r-ggplot2', type=('build', 'run'))
def edit(self, spec, prefix):
config = FileFilter('config-install.txt')
config.filter('PREFIX =.*', 'PREFIX = {0}'.format(prefix))
config.filter('BOWTIE2 PATH =.*',
'BOWTIE2_PATH = {0}'.format(spec['bowtie2'].prefix))
config.filter('SAMTOOLS_PATH =.*',
'SAMTOOLS_PATH = {0}'.format(spec['samtools'].prefix))
config.filter('R_PATH =.*',
'R_RPTH ={0}'.format(spec['r'].prefix))
config.filter('PYTHON_PATH =.*',
'PYTHON_RPTH ={0}'.format(spec['python'].prefix))
def build(self, spec, preifx):
make('-f', './scripts/install/Makefile',
'CONFIG_SYS=./config-install.txt')
make('mapbuilder')
make('readstrimming')
make('iced')
def install(self, spec, prefix):
# Patch INSTALLPATH in config-system.txt
config = FileFilter('config-system.txt')
config.filter('/HiC-Pro_%s' % self.version, '')
# Install
install('config-hicpro.txt', prefix)
install('config-install.txt', prefix)
install('config-system.txt', prefix)
install_tree('bin', prefix.bin)
install_tree('annotation', prefix.annotation)
install_tree('doc', prefix.doc)
install_tree('scripts', prefix.scripts)
install_tree('test-op', join_path(prefix, 'test-op'))
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