68 lines
2.6 KiB
Python
68 lines
2.6 KiB
Python
# Copyright 2013-2024 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 Hybpiper(PythonPackage, Package):
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"""HybPiper was designed for targeted sequence capture, in which DNA
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sequencing libraries are enriched for gene regions of interest,
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especially for phylogenetics. HybPiper is a suite of Python scripts
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that wrap and connect bioinformatics tools in order to extract target
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sequences from high-throughput DNA sequencing reads"""
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homepage = "https://github.com/mossmatters/HybPiper"
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url = "https://github.com/mossmatters/HybPiper/archive/v1.2.0.tar.gz"
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git = "https://github.com/mossmatters/HybPiper/HybPiper.git"
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maintainers("snehring")
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license("GPL-3.0-or-later")
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version("2.1.8", sha256="ff358a560d6dbbec4fdac67457451cb4e6ca21b8661044c43902aa013d805e47")
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version("1.3.1", sha256="7ca07a9390d1ca52c72721774fa220546f18d3fa3b58500f68f3b2d89dbc0ecf")
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version("1.2.0", sha256="34c7b324e9bcacb6ccfe87dc50615d6f93866433b61a59291707efa858b6df57")
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build_system(
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conditional("python_pip", when="@2.1:"),
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conditional("generic", when="@:1.3.1"),
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default="python_pip",
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)
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depends_on("python@2.7:", type=("build", "run"))
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depends_on("python@3.9:", type=("build", "run"), when="@2.1:")
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depends_on("py-biopython", type=("build", "run"))
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depends_on("py-biopython@1.80:", type=("build", "run"), when="@2.1:")
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depends_on("py-matplotlib", type=("build", "run"), when="@2.1:")
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depends_on("py-pandas", type=("build", "run"), when="@2.1:")
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depends_on("py-pebble", type=("build", "run"), when="@2.1:")
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depends_on("py-progressbar2", type=("build", "run"), when="@2.1:")
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depends_on("py-psutil", type=("build", "run"), when="@2.1:")
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depends_on("py-scipy", type=("build", "run"), when="@2.1:")
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depends_on("py-seaborn", type=("build", "run"), when="@2.1:")
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depends_on("exonerate")
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depends_on("exonerate@2.4:", when="@2.1:")
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depends_on("bbmap", when="@2.1:")
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depends_on("blast-plus")
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depends_on("blast-plus@2.9.0:", when="@2.1:")
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depends_on("bwa")
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depends_on("diamond", when="@2.1:")
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depends_on("mafft", when="@2.1:")
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depends_on("parallel")
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depends_on("samtools")
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depends_on("samtools@1.14", when="@2.1:")
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depends_on("spades")
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depends_on("spades@3.15.4:", when="@2.1:")
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def setup_run_environment(self, env):
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env.set("HYBPIPER_HOME", self.prefix)
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@when("@:1.3.1")
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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install("*.py", prefix.bin)
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