old_contents: ##############################################################################
  # Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
  # Produced at the Lawrence Livermore National Laboratory.
  #
  # This file is part of Spack.
  # Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
  # LLNL-CODE-647188
  #
  # For details, see https://github.com/spack/spack
  # Please also see the NOTICE and LICENSE files for our notice and the LGPL.
  #
  # This program is free software; you can redistribute it and/or modify
  # it under the terms of the GNU Lesser General Public License (as
  # published by the Free Software Foundation) version 2.1, February 1999.
  #
  # This program is distributed in the hope that it will be useful, but
  # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
  # conditions of the GNU Lesser General Public License for more details.
  #
  # You should have received a copy of the GNU Lesser General Public
  # License along with this program; if not, write to the Free Software
  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
  ##############################################################################
  from spack import *
  import os
  
  
  class SspaceStandard(Package):
      """SSPACE standard is a stand-alone program for scaffolding pre-assembled
         contigs using NGS paired-read data
  
         Note: A manual download is required for SSPACE-Standard.
         Spack will search your current directory for the download file.
         Alternatively, add this file to a mirror so that Spack can find it.
         For instructions on how to set up a mirror, see
         http://spack.readthedocs.io/en/latest/mirrors.html"""
  
      homepage = "https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE"
      url      = "file://{0}/41SSPACE-STANDARD-3.0_linux-x86_64.tar.gz".format(os.getcwd())
  
      version('3.0', '7e171b4861b9d514e80aafc3d9cdf554')
  
      depends_on('perl+threads', type=('build', 'run'))
  
      def install(self, spec, prefix):
          install_tree('bin', prefix.bin)
          install_tree('bowtie', prefix.bowtie)
          install_tree('bwa', prefix.bwa)
          install_tree('dotlib', prefix.dotlib)
          install_tree('tools', prefix.tools)
          install('SSPACE_Standard_v{0}.pl'.format(self.version), prefix)
  
      def setup_environment(self, spack_env, run_env):
          run_env.set('SSPACE_HOME', prefix)
          run_env.prepend_path('PATH', prefix)
  
new_contents: ##############################################################################
  # Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
  # Produced at the Lawrence Livermore National Laboratory.
  #
  # This file is part of Spack.
  # Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
  # LLNL-CODE-647188
  #
  # For details, see https://github.com/spack/spack
  # Please also see the NOTICE and LICENSE files for our notice and the LGPL.
  #
  # This program is free software; you can redistribute it and/or modify
  # it under the terms of the GNU Lesser General Public License (as
  # published by the Free Software Foundation) version 2.1, February 1999.
  #
  # This program is distributed in the hope that it will be useful, but
  # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
  # conditions of the GNU Lesser General Public License for more details.
  #
  # You should have received a copy of the GNU Lesser General Public
  # License along with this program; if not, write to the Free Software
  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
  ##############################################################################
  from spack import *
  import os
  import glob
  
  
  class SspaceStandard(Package):
      """SSPACE standard is a stand-alone program for scaffolding pre-assembled
         contigs using NGS paired-read data
  
         Note: A manual download is required for SSPACE-Standard.
         Spack will search your current directory for the download file.
         Alternatively, add this file to a mirror so that Spack can find it.
         For instructions on how to set up a mirror, see
         http://spack.readthedocs.io/en/latest/mirrors.html"""
  
      homepage = "https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE"
      url      = "file://{0}/41SSPACE-STANDARD-3.0_linux-x86_64.tar.gz".format(os.getcwd())
  
      version('3.0', '7e171b4861b9d514e80aafc3d9cdf554')
  
      depends_on('perl+threads', type=('build', 'run'))
      depends_on('perl-perl4-corelibs', type=('build', 'run'))
  
      def install(self, spec, prefix):
          rootscript = 'SSPACE_Standard_v{0}.pl'.format(self.version)
  
          scripts = [rootscript]
          scripts.extend(glob.glob('tools/*.pl'))
          scripts.extend(glob.glob('bwa/*.pl'))
  
          for s in scripts:
              filter_file('/usr/bin/perl', '/usr/bin/env perl',
                          s, string=True)
  
          install_tree('bin', prefix.bin)
          install_tree('bowtie', prefix.bowtie)
          install_tree('bwa', prefix.bwa)
          install_tree('dotlib', prefix.dotlib)
          install_tree('tools', prefix.tools)
          install(rootscript, prefix)
  
      def setup_environment(self, spack_env, run_env):
          run_env.set('SSPACE_HOME', prefix)
          run_env.prepend_path('PATH', prefix)
  
subject: add perl-perl4-corelibs dep, fix perl scripts (#9473)