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# Copyright 2013-2024 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 Phyluce(PythonPackage):
"""phyluce (phy-loo-chee) is a software package that was initially
developed for analyzing data collected from ultraconserved
elements in organismal genomes"""
homepage = "https://github.com/faircloth-lab/phyluce"
url = "https://github.com/faircloth-lab/phyluce/archive/v1.6.7.tar.gz"
license("BSD-3-Clause")
version("1.6.7", sha256="98c213ab1610506722ad1440ffc93f9cbc78d8b3aaf3d9a47837e1231452cdb6")
extends("python")
depends_on("python@2.7:", type=("build", "run"))
depends_on("py-setuptools", type=("build", "run"))
depends_on("py-biopython", type="run")
# runtime binary dependencies
depends_on("abyss", type="run")
depends_on("bcftools", type="run")
depends_on("bwa", type="run")
depends_on("gatk", type="run")
depends_on("gblocks", type="run")
depends_on("lastz", type="run")
depends_on("mafft", type="run")
depends_on("muscle", type="run")
depends_on("picard", type="run")
depends_on("raxml+pthreads", type="run")
depends_on("samtools", type="run")
depends_on("seqtk", type="run")
depends_on("spades", type="run")
depends_on("trimal", type="run")
depends_on("trinity", type="run")
depends_on("velvet", type="run")
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