52 lines
1.7 KiB
Python
52 lines
1.7 KiB
Python
# Copyright 2013-2022 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 Angsd(MakefilePackage):
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"""Angsd is a program for analysing NGS data.
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The software can handle a number of different input types from mapped
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reads to imputed genotype probabilities. Most methods take genotype
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uncertainty into account instead of basing the analysis on called
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genotypes. This is especially useful for low and medium depth data.
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"""
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homepage = "https://github.com/ANGSD/angsd"
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url = "https://github.com/ANGSD/angsd/archive/0.935.tar.gz"
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version('0.935', sha256='15000281330fa59ddf745cb84eeaa653acf6da34a4ac6c3df7c5835d1d01ba16')
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version('0.933', sha256='2f992325dc08fa25ac525d9300ef6bd61808e74c521b4cc72a2ce00d98f402bb')
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version('0.921', sha256='8892d279ce1804f9e17fe2fc65a47e5498e78fc1c1cb84d2ca2527fd5c198772')
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version('0.919', sha256='c2ea718ca5a5427109f4c3415e963dcb4da9afa1b856034e25c59c003d21822a')
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variant('r', default=True, description='Enable R dependency')
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depends_on('htslib')
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conflicts('^htslib@1.6:', when='@0.919')
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depends_on('zlib')
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depends_on('lzma')
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depends_on('curl')
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depends_on('r', type='run', when='+r')
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def setup_run_environment(self, env):
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env.set('R_LIBS', self.prefix.R)
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def install(self, spec, prefix):
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binaries = [
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'angsd', 'misc/realSFS', 'misc/thetaStat'
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]
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mkdirp(prefix.bin)
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for b in binaries:
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install(b, join_path(prefix.bin))
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install_tree('R', prefix.R)
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install_tree('RES', prefix.RES)
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install_tree('scripts', prefix.scripts)
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