old_contents: #!/usr/bin/env python3
  
  from setuptools import setup, find_packages
  from somaticseq._version import  __version__ as version
  
  print(version)
  
  setup(
      name='SomaticSeq',
      version=version,
      description='SomaticSeq: An ensemble approach to accurately detect somatic mutations using SomaticSeq',
      author='Li Tai Fang',
      author_email='li_tai.fang@roche.com',
      url='https://github.com/bioinform/somaticseq',
      packages=find_packages(),
      package_data={'': ['*.R']},
      install_requires=['pysam', 'numpy', 'scipy'],
      scripts=['somaticseq/run_somaticseq.py',
               'somaticseq_parallel.py',
               'utilities/dockered_pipelines/makeSomaticScripts.py',
               'utilities/lociCounterWithLabels.py',
               'utilities/split_Bed_into_equal_regions.py']
  )
  
new_contents: #!/usr/bin/env python3
  
  from setuptools import setup, find_packages
  from somaticseq._version import  __version__ as version
  
  print(version)
  
  setup(
      name='SomaticSeq',
      version=version,
      description='SomaticSeq: An ensemble approach to accurately detect somatic mutations using SomaticSeq',
      author='Li Tai Fang',
      author_email='li_tai.fang@roche.com',
      url='https://github.com/bioinform/somaticseq',
      packages=find_packages(),
      package_data={'': ['*.R']},
      install_requires=['pysam', 'numpy', 'scipy'],
      scripts=['somaticseq/run_somaticseq.py',
               'somaticseq_parallel.py',
               'utilities/dockered_pipelines/makeSomaticScripts.py',
               'utilities/lociCounterWithLabels.py',
               'utilities/split_Bed_into_equal_regions.py',
               'somaticseq/somatic_vcf2tsv.py',
               'somaticseq/single_sample_vcf2tsv.py']
  )
  
subject: add useful scripts to exectuable bin