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Diffstat (limited to 'var/spack/repos/builtin/packages/hic-pro/package.py')
-rw-r--r-- | var/spack/repos/builtin/packages/hic-pro/package.py | 61 |
1 files changed, 61 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/hic-pro/package.py b/var/spack/repos/builtin/packages/hic-pro/package.py new file mode 100644 index 0000000000..6cb89d8839 --- /dev/null +++ b/var/spack/repos/builtin/packages/hic-pro/package.py @@ -0,0 +1,61 @@ +# 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 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')) |