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# Copyright 2013-2021 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 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"
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'))
def install(self, spec, prefix):
if self.spec.satisfies('@4.1.3'):
install_tree('bin', prefix.bin)
install_tree('config', prefix.config)
super(self, PythonPackage).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(self, PythonPackage).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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