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 *
  from distutils.dir_util import copy_tree, mkpath
  from distutils.file_util import copy_file
  
  
  class Fastqc(Package):
      """A quality control tool for high throughput sequence data."""
  
      homepage = "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
      url = "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip"
  
      version('0.11.5', '3524f101c0ab0bae77c7595983170a76')
      version('0.11.4', '104ff2e0e9aebf5bee1f6b068a059b0d')
  
      depends_on('java', type='run')
      depends_on('perl')          # for fastqc "script", any perl will do
  
      patch('fastqc.patch', level=0)
  
      def install(self, spec, prefix):
          mkpath(self.prefix.bin)
          mkpath(self.prefix.lib)
          copy_file('fastqc', self.prefix.bin)
          for j in ['cisd-jhdf5.jar', 'jbzip2-0.9.jar', 'sam-1.103.jar']:
              copy_file(j, self.prefix.lib)
          for d in ['Configuration', 'net', 'org', 'Templates', 'uk']:
              copy_tree(d, join_path(self.prefix.lib, d))
          chmod = which('chmod')
          chmod('+x', join_path(self.prefix.bin, 'fastqc'))
  
      # In theory the 'run' dependency on 'jdk' above should take
      # care of this for me. In practice, it does not.
      def setup_environment(self, spack_env, run_env):
          """Add <prefix> to the path; the package has a script at the
             top level.
          """
          run_env.prepend_path('PATH', join_path(self.spec['java'].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 *
  from distutils.dir_util import copy_tree, mkpath
  from distutils.file_util import copy_file
  
  
  class Fastqc(Package):
      """A quality control tool for high throughput sequence data."""
  
      homepage = "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
      url = "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip"
  
      version('0.11.7', '8fead05fa62c5e723f0d2157a9b5fcd4')
      version('0.11.5', '3524f101c0ab0bae77c7595983170a76')
      version('0.11.4', '104ff2e0e9aebf5bee1f6b068a059b0d')
  
      depends_on('java', type='run')
      depends_on('perl')          # for fastqc "script", any perl will do
  
      patch('fastqc.patch', level=0)
  
      def install(self, spec, prefix):
          mkpath(self.prefix.bin)
          mkpath(self.prefix.lib)
          copy_file('fastqc', self.prefix.bin)
          for j in ['cisd-jhdf5.jar', 'jbzip2-0.9.jar', 'sam-1.103.jar']:
              copy_file(j, self.prefix.lib)
          for d in ['Configuration', 'net', 'org', 'Templates', 'uk']:
              copy_tree(d, join_path(self.prefix.lib, d))
          chmod = which('chmod')
          chmod('+x', join_path(self.prefix.bin, 'fastqc'))
  
      # In theory the 'run' dependency on 'jdk' above should take
      # care of this for me. In practice, it does not.
      def setup_environment(self, spack_env, run_env):
          """Add <prefix> to the path; the package has a script at the
             top level.
          """
          run_env.prepend_path('PATH', join_path(self.spec['java'].prefix,
                               'bin'))
  
subject: Add version 0.11.7 (#8319)