old_contents: # Copyright 2013-2020 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 = "http://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"
  
      # 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')
  
      depends_on('python', type=('build', 'run'))
      depends_on('blast-plus')
      depends_on('hmmer')
      depends_on('augustus')
  
      def build(self, spec, prefix):
          if self.spec.satisfies('@2.0.1'):
              pass
  
      def install(self, 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)
              args = self.install_args(spec, prefix)
              self.setup_py('install', *args)
          if self.spec.satisfies('@2.0.1'):
              mkdirp(prefix.bin)
              install('BUSCO.py', prefix.bin)
              install('BUSCO_plot.py', prefix.bin)
  
new_contents: # Copyright 2013-2020 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 = "http://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')
  
      depends_on('python', type=('build', 'run'))
      depends_on('blast-plus')
      depends_on('hmmer')
      depends_on('augustus')
  
      depends_on('py-biopython', when='@4.1.3', type=('build', 'run'))
  
      def build(self, spec, prefix):
          if self.spec.satisfies('@2.0.1'):
              pass
  
      def install(self, spec, prefix):
          if self.spec.satisfies('@4.1.3'):
              install_tree('bin', prefix.bin)
              install_tree('config', prefix.config)
              args = self.install_args(spec, prefix)
              self.setup_py('install', *args)
          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)
              args = self.install_args(spec, prefix)
              self.setup_py('install', *args)
          if self.spec.satisfies('@2.0.1'):
              mkdirp(prefix.bin)
              install('BUSCO.py', prefix.bin)
              install('BUSCO_plot.py', prefix.bin)
  
subject: add 4.1.3 (#19296)