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# Copyright 2013-2023 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.package import *
class Hybpiper(Package):
"""HybPiper was designed for targeted sequence capture, in which DNA
sequencing libraries are enriched for gene regions of interest,
especially for phylogenetics. HybPiper is a suite of Python scripts
that wrap and connect bioinformatics tools in order to extract target
sequences from high-throughput DNA sequencing reads"""
homepage = "https://github.com/mossmatters/HybPiper"
url = "https://github.com/mossmatters/HybPiper/archive/v1.2.0.tar.gz"
git = "https://github.com/mossmatters/HybPiper/HybPiper.git"
version("1.3.1", sha256="7ca07a9390d1ca52c72721774fa220546f18d3fa3b58500f68f3b2d89dbc0ecf")
version("1.2.0", sha256="34c7b324e9bcacb6ccfe87dc50615d6f93866433b61a59291707efa858b6df57")
depends_on("python@2.7:", type=("build", "run"))
depends_on("py-biopython", type=("build", "run"))
depends_on("exonerate")
depends_on("blast-plus")
depends_on("spades")
depends_on("parallel")
depends_on("bwa")
depends_on("samtools")
def setup_run_environment(self, env):
env.set("HYBPIPER_HOME", self.prefix)
def install(self, spec, prefix):
mkdirp(prefix.bin)
install("*.py", prefix.bin)
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