old_contents: # 
  # Author    : Manuel Bernal Llinares
  # Project   : trackhub-creator
  # Timestamp : 01-07-2017 23:20
  # ---
  # © 2017 Manuel Bernal Llinares <mbdebian@gmail.com>
  # All rights reserved.
  # 
  
  """
  This module runs PoGo for a file, using the given GTF and FA reference files, it will produce the results in the same
  folder where the input file is located
  """
  
  import config_manager
  import toolbox
  # From this application
  import pipelines.template_pipeline as template_pipeline
  
  __configuration_file = None
  __configuration_manager = None
  
  
  def __get_configuration_manager():
      global __configuration_manager
      if __configuration_manager is None:
          __configuration_manager = DirectorConfigurationManager(toolbox.read_json(__configuration_file),
                                                                 __configuration_file)
      return __configuration_manager
  
  
  class DirectorConfigurationManager(config_manager.ConfigurationManager):
      def __init__(self, configuration_object, configuration_file):
          super(DirectorConfigurationManager, self).__init__(configuration_object, configuration_file)
  
  
  # Pipeline Director
  class Director(template_pipeline.Director):
      def __init__(self, config_file_name, runner_id=0):
          super(Director, self).__init__(config_file_name, runner_id)
          self._set_logger(config_manager.get_app_config_manager().get_logger_for(__name__))
  
      def _run_pipeline(self):
          # TODO
          pass
  
  
  if __name__ == '__main__':
      print("ERROR: This script is part of a pipeline collection and it is not met to be run in stand alone mode")
  
new_contents: # 
  # Author    : Manuel Bernal Llinares
  # Project   : trackhub-creator
  # Timestamp : 01-07-2017 23:20
  # ---
  # © 2017 Manuel Bernal Llinares <mbdebian@gmail.com>
  # All rights reserved.
  # 
  
  """
  This module runs PoGo for a file, using the given GTF and FA reference files, it will produce the results in the same
  folder where the input file is located
  """
  
  # App imports
  import config_manager
  import toolbox
  import pipelines.template_pipeline as template_pipeline
  
  __configuration_file = None
  __configuration_manager = None
  
  
  def __get_configuration_manager():
      global __configuration_manager
      if __configuration_manager is None:
          __configuration_manager = DirectorConfigurationManager(toolbox.read_json(__configuration_file),
                                                                 __configuration_file)
      return __configuration_manager
  
  
  class DirectorConfigurationManager(config_manager.ConfigurationManager):
      def __init__(self, configuration_object, configuration_file):
          super(DirectorConfigurationManager, self).__init__(configuration_object, configuration_file)
  
  
  # Pipeline Director
  class Director(template_pipeline.Director):
      def __init__(self, config_file_name, runner_id=0):
          super(Director, self).__init__(config_file_name, runner_id)
          self._set_logger(config_manager.get_app_config_manager().get_logger_for(__name__))
  
      def _run_pipeline(self):
          # TODO
          pass
  
  
  if __name__ == '__main__':
      print("ERROR: This script is part of a pipeline collection and it is not met to be run in stand alone mode")
  
subject: comment correction