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', 'pandas', 'xgboost'],
      scripts=['somaticseq_parallel.py',
               'somaticseq/run_somaticseq.py',
               'somaticseq/single_sample_vcf2tsv.py',
               'somaticseq/somatic_vcf2tsv.py',
               'somaticseq/somatic_xgboost.py',
               'somaticseq/SSeq_tsv2vcf.py',
               'utilities/attach_pileupVAF.py',
               'utilities/bamQC.py',
               'utilities/linguistic_sequence_complexity.py',
               'utilities/lociCounterWithLabels.py',
               'utilities/remove_callers_from_somaticseq_tsv.py',
               'utilities/split_Bed_into_equal_regions.py',
               'utilities/tally_variants_from_multiple_vcfs.py',
               'utilities/variant_annotation.py',
               'utilities/vcfsorter.pl',
               'utilities/makeAlignmentScripts.py',
               'utilities/dockered_pipelines/makeSomaticScripts.py',
               'r_scripts/ada_model_builder_ntChange.R',
               'r_scripts/ada_model_predictor.R',
               ]
  )
  
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', 'pandas', 'xgboost'],
      scripts=['somaticseq_parallel.py',
               'somaticseq/run_somaticseq.py',
               'somaticseq/single_sample_vcf2tsv.py',
               'somaticseq/somatic_vcf2tsv.py',
               'somaticseq/somatic_xgboost.py',
               'somaticseq/SSeq_tsv2vcf.py',
               'utilities/attach_pileupVAF.py',
               'utilities/bamQC.py',
               'utilities/linguistic_sequence_complexity.py',
               'utilities/lociCounterWithLabels.py',
               'utilities/remove_callers_from_somaticseq_tsv.py',
               'utilities/split_Bed_into_equal_regions.py',
               'utilities/tally_variants_from_multiple_vcfs.py',
               'utilities/variant_annotation.py',
               'utilities/vcfsorter.pl',
               'utilities/dockered_pipelines/makeAlignmentScripts.py',
               'utilities/dockered_pipelines/makeSomaticScripts.py',
               'r_scripts/ada_model_builder_ntChange.R',
               'r_scripts/ada_model_predictor.R',
               ]
  )
  
subject: add alignment workflow to setup