text: # Copyright 2013-2022 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)
  
  import os
  import shutil
  
  from spack import *
  
  
  class Orthofinder(Package):
      """OrthoFinder is a fast, accurate and comprehensive analysis tool for
      comparative genomics.
  
      It finds orthologues and orthogroups infers rooted  gene trees for all
      orthogroups and infers a rooted species tree for the species being
      analysed. OrthoFinder also provides comprehensive statistics for
      comparative genomic analyses. OrthoFinder is simple to use and all you
      need to run it is a set of protein sequence files (one per species)
      in FASTA format."""
  
      homepage = "https://github.com/davidemms/OrthoFinder"
      url = "https://github.com/davidemms/OrthoFinder/releases/download/2.5.2/OrthoFinder_source.tar.gz"
  
      version('2.5.4', sha256='a735c81999e8e3026ad62536b14e5b0391c9fc632f872f99857936ac60003ba5')
      version('2.5.2', sha256='e0752b66866e23a11f0592e880fac5f67258f9cf926f926dec8849564c41b8f7')
      version('2.2.0', sha256='375f711086b44e2118d7d460821294744245e254e5fa2151dfe73100c0707a8c')
  
      depends_on('py-numpy', type='run')
      depends_on('py-scipy', type='run')
      depends_on('diamond', type='run')
      depends_on('blast-plus', type='run')
      depends_on('mcl', type='run')
      depends_on('fastme', type='run')
  
      def url_for_version(self, version):
          if '@:2.3.6' in self.spec:
              url = "https://github.com/davidemms/OrthoFinder/releases/download/{0}/OrthoFinder-{0}_source.tar.gz"
              return url.format(version)
          else:
              url = "https://github.com/davidemms/OrthoFinder/releases/download/{0}/OrthoFinder_source.tar.gz"
              return url.format(version)
  
      def install(self, spec, prefix):
          if '@2.2.0' in spec:
              install_tree('./orthofinder', prefix.bin)
          else:
              install_tree('.', prefix.bin)
              shutil.rmtree(prefix.bin.scripts_of.bin)
          os.rename('%s/orthofinder.py' % prefix.bin, '%s/orthofinder' % prefix.bin)
  
      def setup_run_environment(self, env):
          env.prepend_path('PATH', prefix.bin)
          env.prepend_path('PATH', prefix.bin.tools)
  