old_contents: # Copyright 2013-2019 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 Braker(Package):
      """BRAKER is a pipeline for unsupervised RNA-Seq-based genome annotation
         that combines the advantages of GeneMark-ET and AUGUSTUS"""
  
      homepage = "http://exon.gatech.edu/braker1.html"
      url      = "http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER_v2.1.0.tar.gz"
      list_url = "http://bioinf.uni-greifswald.de/augustus/binaries/old"
  
      version('2.1.0', '5f974abcceb9f96a11668fa20a6f6a56')
      version('1.11', '297efe4cabdd239b710ac2c45d81f6a5',
              url='http://bioinf.uni-greifswald.de/augustus/binaries/old/BRAKER1_v1.11.tar.gz')
  
      depends_on('perl', type=('build', 'run'))
      depends_on('perl-scalar-util-numeric', type=('build', 'run'))
      depends_on('perl-parallel-forkmanager', type=('build', 'run'))
      depends_on('perl-file-which', type=('build', 'run'))
      depends_on('augustus@3.2.3')
      depends_on('genemark-et')
      depends_on('bamtools')
      depends_on('samtools')
  
      def install(self, spec, prefix):
          mkdirp(prefix.bin)
          mkdirp(prefix.lib)
          install('braker.pl', prefix.bin)
          install('filterGenemark.pl', prefix.bin)
          install('filterIntronsFindStrand.pl', prefix.bin)
          install('helpMod.pm', prefix.lib)
  
      def setup_environment(self, spack_env, run_env):
          run_env.prepend_path('PERL5LIB', prefix.lib)
  
new_contents: # Copyright 2013-2019 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 *
  import os
  import glob
  
  
  class Braker(Package):
      """BRAKER is a pipeline for unsupervised RNA-Seq-based genome annotation
         that combines the advantages of GeneMark-ET and AUGUSTUS"""
  
      homepage = "http://exon.gatech.edu/braker1.html"
      url      = "https://github.com/Gaius-Augustus/BRAKER/archive/v2.1.4.tar.gz"
      list_url = "http://bioinf.uni-greifswald.de/augustus/binaries/old"
  
      version('2.1.4', sha256='d48af5649cc879343046f9ddf180fe2c709b5810e0b78cf314bf298514d31d52')
      version('2.1.0', '5f974abcceb9f96a11668fa20a6f6a56')
      version('1.11', '297efe4cabdd239b710ac2c45d81f6a5',
              url='http://bioinf.uni-greifswald.de/augustus/binaries/old/BRAKER1_v1.11.tar.gz')
  
      depends_on('perl', type=('build', 'run'))
      depends_on('perl-scalar-util-numeric', type=('build', 'run'))
      depends_on('perl-parallel-forkmanager', type=('build', 'run'))
      depends_on('perl-file-which', type=('build', 'run'))
      depends_on('perl-yaml', type=('build', 'run'))
      depends_on('perl-hash-merge', type=('build', 'run'))
      depends_on('perl-logger-simple', type=('build', 'run'))
      depends_on('perl-file-homedir', when='@2.1.4:', type=('build', 'run'))
      depends_on('augustus')
      depends_on('augustus@3.2.3', when='@:2.1.0')
      depends_on('genemark-et')
      depends_on('bamtools')
      depends_on('samtools')
  
      def install(self, spec, prefix):
          mkdirp(prefix.bin)
          mkdirp(prefix.lib)
          if self.version < Version('2.1.2'):
              install('braker.pl', prefix.bin)
              install('filterGenemark.pl', prefix.bin)
              install('filterIntronsFindStrand.pl', prefix.bin)
              install('helpMod.pm', prefix.lib)
          else:
              install_tree('docs', prefix.docs)
              install_tree('example', prefix.example)
              with working_dir('scripts'):
                  install('helpMod.pm', prefix.lib)
                  files = glob.iglob('*.pl')
                  for file in files:
                      if os.path.isfile(file):
                          install(file, prefix.bin)
  
      @run_after('install')
      def filter_sbang(self):
          with working_dir(self.prefix.bin):
              pattern = '^#!.*/usr/bin/env perl'
              repl = '#!{0}'.format(self.spec['perl'].command.path)
              files = glob.iglob("*.pl")
              for file in files:
                  filter_file(pattern, repl, *files, backup=False)
  
      def setup_environment(self, spack_env, run_env):
          run_env.prepend_path('PERL5LIB', prefix.lib)
  
subject: Update braker package