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 *
  
  
  class Trimgalore(Package):
      """Trim Galore! is a wrapper around Cutadapt and FastQC to consistently
         apply adapter and quality trimming to FastQ files, with extra
         functionality for RRBS data."""
  
      homepage = "https://github.com/FelixKrueger/TrimGalore"
      url      = "https://github.com/FelixKrueger/TrimGalore/archive/0.4.4.tar.gz"
  
      version('0.4.5', 'c71756042b2a65c34d483533a29dc206')
      version('0.4.4', 'aae1b807b48e38bae7074470203997bb')
  
      depends_on('perl', type=('build', 'run'))
      depends_on('py-cutadapt', type=('build', 'run'))
      depends_on('fastqc')
  
      def install(self, spec, prefix):
          mkdirp(prefix.bin)
          install('trim_galore', prefix.bin)
  
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 *
  
  
  class Trimgalore(Package):
      """Trim Galore! is a wrapper around Cutadapt and FastQC to consistently
         apply adapter and quality trimming to FastQ files, with extra
         functionality for RRBS data."""
  
      homepage = "https://github.com/FelixKrueger/TrimGalore"
      url      = "https://github.com/FelixKrueger/TrimGalore/archive/0.4.4.tar.gz"
  
      version('0.4.5', 'c71756042b2a65c34d483533a29dc206')
      version('0.4.4', 'aae1b807b48e38bae7074470203997bb')
  
      depends_on('perl', type=('build', 'run'))
      depends_on('py-cutadapt', type=('build', 'run'))
      depends_on('fastqc')
  
      def install(self, spec, prefix):
          filter_file(r'#!/usr/bin/perl', '#!/usr/bin/env perl', 'trim_galore')
  
          mkdirp(prefix.bin)
          install('trim_galore', prefix.bin)
  
subject: Use perl from env (#8318)