62927654dd
We'd like to use a consistent checksum scheme everywhere so that we can:
a) incorporate archive checksums into our specs and have a
consistent hashing algorithm across all specs.
b) index mirrors with a consistent type of checksum, and not one that
is dependent on how spack packages are written.
- [x] convert existing md5, sha224, sha512, sha1 checksums to sha256
62 lines
2.4 KiB
Python
62 lines
2.4 KiB
Python
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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class HicPro(MakefilePackage):
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"""HiC-Pro is a package designed to process Hi-C data,
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from raw fastq files (paired-end Illumina data)
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to the normalized contact maps"""
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homepage = "https://github.com/nservant/HiC-Pro"
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url = "https://github.com/nservant/HiC-Pro/archive/v2.10.0.tar.gz"
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version('2.10.0', sha256='df181ea5c57247caf6b25fd15dfbb03df597ff8c4f57599d88607648bb61f1b7')
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depends_on('bowtie2')
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depends_on('samtools')
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depends_on('python+ucs4@2.7:2.8')
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depends_on('r')
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depends_on('py-numpy', type=('build', 'run'))
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depends_on('py-scipy', type=('build', 'run'))
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depends_on('py-pysam', type=('build', 'run'))
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depends_on('py-bx-python', type=('build', 'run'))
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depends_on('r-rcolorbrewer', type=('build', 'run'))
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depends_on('r-ggplot2', type=('build', 'run'))
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def edit(self, spec, prefix):
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config = FileFilter('config-install.txt')
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config.filter('PREFIX =.*', 'PREFIX = {0}'.format(prefix))
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config.filter('BOWTIE2 PATH =.*',
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'BOWTIE2_PATH = {0}'.format(spec['bowtie2'].prefix))
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config.filter('SAMTOOLS_PATH =.*',
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'SAMTOOLS_PATH = {0}'.format(spec['samtools'].prefix))
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config.filter('R_PATH =.*',
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'R_RPTH ={0}'.format(spec['r'].prefix))
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config.filter('PYTHON_PATH =.*',
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'PYTHON_RPTH ={0}'.format(spec['python'].prefix))
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def build(self, spec, preifx):
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make('-f', './scripts/install/Makefile',
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'CONFIG_SYS=./config-install.txt')
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make('mapbuilder')
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make('readstrimming')
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make('iced')
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def install(self, spec, prefix):
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# Patch INSTALLPATH in config-system.txt
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config = FileFilter('config-system.txt')
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config.filter('/HiC-Pro_%s' % self.version, '')
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# Install
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install('config-hicpro.txt', prefix)
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install('config-install.txt', prefix)
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install('config-system.txt', prefix)
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install_tree('bin', prefix.bin)
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install_tree('annotation', prefix.annotation)
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install_tree('doc', prefix.doc)
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install_tree('scripts', prefix.scripts)
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install_tree('test-op', join_path(prefix, 'test-op'))
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