50 lines
1.7 KiB
Python
50 lines
1.7 KiB
Python
# Copyright 2013-2023 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.package 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 = ["angsd", "misc/realSFS", "misc/thetaStat"]
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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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