old_contents: #!/usr/bin/env python
  
  """Setup file and install script for NextGen sequencing analysis scripts"""
  
  import os
  import subprocess
  
  import setuptools
  
  VERSION = '1.2.3'
  
  # add bcbio version number and git commit hash of the current revision to version.py
  try:
      git_run = subprocess.run(['git', 'rev-parse', '--short', 'HEAD'], stdout=subprocess.PIPE)
      git_run.check_returncode()
  except subprocess.SubprocessError:
      commit_hash = ''
  else:
      commit_hash = git_run.stdout.strip().decode()
  
  here = os.path.dirname(os.path.abspath(__file__))
  with open(os.path.join(here, 'bcbio', 'pipeline', 'version.py'), 'w') as version_file:
      version_file.writelines([f'__version__ = "{VERSION}"\n',
                               f'__git_revision__ = "{commit_hash}"\n'])
  
  # dependencies are installed via Conda from
  # https://github.com/chapmanb/cloudbiolinux/blob/master/contrib/flavor/ngs_pipeline_minimal/packages-conda.yaml
  setuptools.setup(version=VERSION)
  
new_contents: #!/usr/bin/env python
  
  """Setup file and install script for NextGen sequencing analysis scripts"""
  
  import os
  import subprocess
  
  import setuptools
  
  VERSION = '1.2.3'
  
  # add bcbio version number and git commit hash of the current revision to version.py
  try:
      git_run = subprocess.run(['git', 'rev-parse', '--short', 'HEAD'], stdout=subprocess.PIPE)
      git_run.check_returncode()
  except subprocess.SubprocessError:
      commit_hash = ''
  else:
      commit_hash = git_run.stdout.strip().decode()
  
  here = os.path.dirname(os.path.abspath(__file__))
  with open(os.path.join(here, 'bcbio', 'pipeline', 'version.py'), 'w') as version_file:
      version_file.writelines([f'__version__ = "{VERSION}"\n',
                               f'__git_revision__ = "{commit_hash}"\n'])
  
  # dependencies are installed via Conda from
  # https://github.com/chapmanb/cloudbiolinux/blob/master/contrib/flavor/ngs_pipeline_minimal/packages-conda.yaml
  setuptools.setup(
      name='bcbio',
      script_name='bcbio_nextgen.py',
      version=VERSION,
      packages=['bcbio'],
      include_package_data=True,
      zip_safe=False,
      scripts=[
          os.path.join('scripts', 'bcbio_nextgen.py'),
      ],
  )
  
subject: Add "script" and "packages" into setup.py to enable `pip install -e` for development