new_contents: ##############################################################################
  # Copyright (c) 2013-2016, 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/llnl/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 Ampliconnoise(MakefilePackage):
      """AmpliconNoise is a collection of programs for the removal of noise
         from 454 sequenced PCR amplicons."""
  
      homepage = "https://code.google.com/archive/p/ampliconnoise/"
      url      = "https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/ampliconnoise/AmpliconNoiseV1.29.tar.gz"
  
      version('1.29', 'd6723e6f9cc71d7eb6f1a65ba4643aac')
  
      depends_on('mpi@2:')
      depends_on('gsl')
  
      def setup_environment(self, spack_env, run_env):
          run_env.prepend_path('PATH', self.prefix.Scripts)
          run_env.set('PYRO_LOOKUP_FILE', join_path(self.prefix, 'Data',
                      'LookUp_E123.dat'))
          run_env.set('SEQ_LOOKUP_FILE', join_path(self.prefix, 'Data',
                      'Tran.dat'))
  
      def install(self, spec, prefix):
          make('install')
          install_tree('bin', prefix.bin)
          install_tree('Data', prefix.Data)
          install_tree('FastaUnique', prefix.FastaUnique)
          install_tree('FCluster', prefix.FCluster)
          install_tree('NDist', prefix.NDist)
          install_tree('Perseus', prefix.Perseus)
          install_tree('PerseusD', prefix.PerseusD)
          install_tree('PyroDist', prefix.PyroDist)
          install_tree('PyroNoise', prefix.PyroNoise)
          install_tree('PyroNoiseM', prefix.PyroNoiseM)
          install_tree('Scripts', prefix.Scripts)
          install_tree('SeqDist', prefix.SeqDist)
          install_tree('SeqNoise', prefix.SeqNoise)
          install_tree('SplitClusterClust', prefix.SplitClusterClust)
          install_tree('SplitClusterEven', prefix.SplitClusterEven)
          install_tree('Test', prefix.Test)
          install_tree('TestFLX', prefix.TestFLX)
          install_tree('TestTitanium', prefix.TestTitanium)
          install_tree('TestTitaniumFast', prefix.TestTitaniumFast)
  
subject: Package ampliconnoise (#4676)