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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 Busco(PythonPackage):
"""Assesses genome assembly and annotation completeness with Benchmarking
Universal Single-Copy Orthologs"""
homepage = "https://busco.ezlab.org/"
url = "https://gitlab.com/api/v4/projects/ezlab%2Fbusco/repository/archive.tar.gz?sha=2.0.1"
git = "https://gitlab.com/ezlab/busco.git"
maintainers("snehring")
license("MIT")
version("5.4.3", sha256="8b92dcc32691f7c1629aaaa7bd54f96073273ba7de5a3a8586fe552c51a9d36a")
version("4.1.3", sha256="08ded26aeb4f6aef791cd88524c3c00792a054c7672ea05219f468d495e7b072")
# TODO: check the installation procedure for version 3.0.2
# and uncomment the following line
# version('3.0.2', sha256='dbea093315b766b0f7c4fe3cafbbdf51ade79ec84bde04f1f437b48333200f34')
# There is no tag for version 3.0.1
version("3.0.1", commit="078252e00399550d7b0e8941cd4d986c8e868a83")
version("2.0.1", sha256="bd72a79b880370e9b61b8c722e171818c7c85d46cc1e2f80595df2738a7e220c")
# https://busco.ezlab.org/busco_userguide.html#manual-installation
depends_on("python@3.3:", when="@4:", type=("build", "run"))
# pip silently replaces distutils with setuptools
depends_on("py-setuptools", when="@3:", type="build")
depends_on("blast-plus")
depends_on("hmmer")
depends_on("augustus")
depends_on("py-biopython", when="@4.1.3:", type=("build", "run"))
depends_on("py-pandas", when="@5:", type="run")
depends_on("bbmap", when="@5:", type="run")
depends_on("prodigal", when="@5:", type="run")
depends_on("metaeuk", when="@5:", type="run")
depends_on("sepp", when="@5:", type="run")
def install(self, spec, prefix):
if self.spec.satisfies("@4.1.3:"):
install_tree("bin", prefix.bin)
install_tree("config", prefix.config)
super().install(spec, prefix)
if self.spec.satisfies("@3.0.1"):
with working_dir("scripts"):
mkdirp(prefix.bin)
install("generate_plot.py", prefix.bin)
install("run_BUSCO.py", prefix.bin)
install_tree("config", prefix.config)
super().install(spec, prefix)
if self.spec.satisfies("@2.0.1"):
mkdirp(prefix.bin)
install("BUSCO.py", prefix.bin)
install("BUSCO_plot.py", prefix.bin)
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