new_contents: #!/bin/env python
  
  """ pipeline_quickstart_stages_config.py
  
      -Configuration file to set options specific to each stage/task in pipeline_quickstart.py
  =============================================================================
  """
  import os
  
  import QuickstartUserInput as I
  
  import WitsgwasSoftware as SW
  
  # python = SW.python
  # plink = SW.plink
  # plink1 = SW.plink1
  # perl = SW.perl
  # R = SW.R
  
  
  # stageDefaults contains the default options which are applied to each stage (command).
  # This section is required for every Rubra pipeline.
  # These can be overridden by options defined for individual stages, below.
  # Stage options which Rubra will recognise are: 
  #  - distributed: a boolean determining whether the task should be submitted to a cluster
  #      job scheduling system (True) or run on the system local to Rubra (False). 
  #  - walltime: for a distributed PBS job, gives the walltime requested from the job
  #      queue system; the maximum allowed runtime. For local jobs has no effect.
  #  - memInGB: for a distributed PBS job, gives the memory in Gigabytes requested from the 
  #      job queue system. For local jobs has no effect.
  #  - queue: for a distributed PBS job, this is the name of the queue to submit the
  #      job to. For local jobs has no effect. This is currently a mandatory field for
  #      distributed jobs, but can be set to None.
  #  - modules: the modules to be loaded before running the task. This is intended for  
  #      systems with environment modules installed. Rubra will call module load on each 
  #      required module before running the task. Note that defining modules for individual 
  #      stages will override (not add to) any modules listed here. This currently only
  #      works for distributed jobs.
  
  
  
  stageDefaults = {
      'distributed': True,
      'queue': 'WitsLong',
      'walltime': "6:00:00",
      'memInGB': 16,
      'name': None,
      'modules': [
  #         python,
  #         plink,
  #         perl,
  #         R,
            'gwaspipe',
      ]
  }
  
  
  
  # stages should hold the details of each stage which can be called by runStageCheck.
  # This section is required for every Rubra pipeline.
  # Calling a stage in this way carries out checkpointing and, if desired, batch job
  # submission. 
  # Each stage must contain a 'command' definition. See stageDefaults above for other 
  # allowable options.
  
  
  stages = {
  	'task1': {
  		"command": ""
  	},
  	'task2': {
  		"command": ""
  	},
  	'task3': {
  		'command': ""
  	},
  }
  
subject: Create pipeline_quickstart_stages_config.py