81 lines
3.4 KiB
Python
81 lines
3.4 KiB
Python
##############################################################################
|
|
# 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'))
|