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##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
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', '6ae2213dcc984b722d1a1f65fcbb21a2')
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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