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# Copyright 2013-2022 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.package 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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