old_contents: """Description
  
  Setup script to install genomics/bcftbx
  
  Copyright (C) University of Manchester 2011-15 Peter Briggs
  
  """
  
  # Hack to acquire all scripts that we want to
  # install into 'bin'
  from glob import glob
  scripts = []
  for pattern in ('build-indexes/*.sh',
                  'ChIP-seq/*.pl','ChIP-seq/*.py',
                  'illumina2cluster/*.py','illumina2cluster/*.sh',
                  'microarray/*.py',
                  'NGS-general/*.pl','NGS-general/*.py','NGS-general/*.py',
                  'QC-pipeline/*.py','QC-pipeline/*.sh',
                  'RNA-seq/*.py',
                  'solid2cluster/*.py','solid2cluster/*.sh',
                  'utils/*.pl','utils/*.py','utils/*.R','utils/*.sh',
                  'share/bcftbx.*.sh'):
      scripts.extend(glob(pattern))
  
  # Setup for installation etc
  from setuptools import setup
  import bcftbx
  setup(name = "genomics",
        version = bcftbx.__version__,
        description = 'Utilities for NGS and genomic bioinformatics',
        long_description = """Utility programs and libraries used for Next Generation
        Sequencing (NGS) and genomic bioinformatics, developed and used within the
        Bioinformatics Core Facility (BCF) at the University of Manchester""",
        url = 'https://github.com/fls-bioinformatics-core/genomics',
        maintainer = 'Peter Briggs',
        maintainer_email = 'peter.briggs@manchester.ac.uk',
        packages = ['bcftbx','bcftbx.qc'],
        license = 'Artistic License',
        # Pull in dependencies
        install_requires = ['xlwt >= 0.7.2',
                            'xlrd >= 0.7.1',
                            'xlutils >= 1.4.1'],
        # Enable 'python setup.py test'
        test_suite='nose.collector',
        tests_require=['nose'],
        scripts = scripts,
        include_package_data=True,
        zip_safe = False)
  
new_contents: """Description
  
  Setup script to install genomics/bcftbx
  
  Copyright (C) University of Manchester 2011-15 Peter Briggs
  
  """
  
  # Hack to acquire all scripts that we want to
  # install into 'bin'
  from glob import glob
  scripts = []
  for pattern in ('build-indexes/*.sh',
                  'ChIP-seq/*.pl','ChIP-seq/*.py',
                  'illumina2cluster/*.py','illumina2cluster/*.sh',
                  'microarray/*.py',
                  'NGS-general/*.pl','NGS-general/*.py','NGS-general/*.py',
                  'QC-pipeline/*.py','QC-pipeline/*.sh',
                  'RNA-seq/*.py',
                  'solid2cluster/*.py','solid2cluster/*.sh',
                  'utils/*.pl','utils/*.py','utils/*.R','utils/*.sh',
                  'share/bcftbx.*.sh'):
      scripts.extend(glob(pattern))
  
  # Setup for installation etc
  from setuptools import setup
  import bcftbx
  setup(name = "genomics",
        version = bcftbx.__version__,
        description = 'Utilities for NGS and genomic bioinformatics',
        long_description = """Utility programs and libraries used for Next Generation
        Sequencing (NGS) and genomic bioinformatics, developed and used within the
        Bioinformatics Core Facility (BCF) at the University of Manchester""",
        url = 'https://github.com/fls-bioinformatics-core/genomics',
        maintainer = 'Peter Briggs',
        maintainer_email = 'peter.briggs@manchester.ac.uk',
        packages = ['bcftbx','bcftbx.qc'],
        license = 'Artistic License',
        # Pull in dependencies
        install_requires = ['xlwt >= 0.7.2',
                            'xlrd >= 0.7.1',
                            'xlutils >= 1.4.1'],
        # Enable 'python setup.py test'
        test_suite='nose.collector',
        tests_require=['nose'],
        # Scripts
        scripts = scripts,
        # Configuration file for QC
        data_files = ['config',['QC-pipeline/qc.setup.sample']],
        include_package_data=True,
        zip_safe = False)
  
subject: add qc.setup.sample to the data files for the package.