old_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  # @Author: oesteban
  # @Date:   2016-03-16 11:28:27
  # @Last Modified by:   oesteban
  # @Last Modified time: 2016-03-16 15:12:13
  
  """
  Agave app generator
  
  """
  import json
  from argparse import ArgumentParser, RawTextHelpFormatter
  import mriqc
  
  agaveapp = {
      'name': mriqc.__name__,
      'version': mriqc.__version__.split('.')[:3],
      'helpURI': 'http://mriqc.readthedocs.org',
      'label': 'mriqc',
      'shortDescription': mriqc.__description__,
      'longDescription': mriqc.__longdesc__,
      'executionSystem': 'slurm-stampede.tacc.utexas.edu',
      'executionType': 'HPC',
      'parallelism': 'PARALLEL',
      'defaultQueue': 'normal',
      'defaultNodeCount': 1,
      'deploymentPath': 'apps/mriqc',
      'deploymentSystem': 'openfmri-storage',
      'templatePath': 'wrapper.sh',
      'testPath': 'test/test.sh',
      'tags': ['qc', 'sMRI', 'fMRI'],
      'modules': [],
      'inputs': [{
          'id': 'bidsFolder',
          'details': {
              'label': 'folder',
              'description': 'input root folder of a BIDS-compliant tree',
              'argument': None,
              'showArgument': False
          },
          'value': {
              'visible': True,
              'required': True,
              'type': 'string'
          },
          'semantics': {
              'ontology': []
          }
      }],
      'parameters': [],
      'checkpointable': False
  }
  
  def main():
      """Entry point"""
  
      parser = ArgumentParser(description='ABIDE2BIDS downloader',
                              formatter_class=RawTextHelpFormatter)
  #    g_inputs = parser.add_argument_group('Inputs')
  #    g_inputs.add_argument('--help-uri', action='store')
  
      g_outputs = parser.add_argument_group('Outputs')
      g_outputs.add_argument('-o', '--output', action='store',
                             default='app.json')
  
      opts = parser.parse_args()
  
      with open(opts.output, 'w') as appfile:
          json.dump(agaveapp, appfile, indent=4)
  
  
  
  if __name__ == '__main__':
      main()
  
new_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  # @Author: oesteban
  # @Date:   2016-03-16 11:28:27
  # @Last Modified by:   oesteban
  # @Last Modified time: 2016-03-16 15:12:13
  
  """
  Agave app generator
  
  """
  import json
  from argparse import ArgumentParser, RawTextHelpFormatter
  import mriqc
  
  version = '.'.join([v for v in mriqc.__version__.split('.') if v.isdigit()])
  if len(version.split('.')) > 3:
      version = '.'.join(version.split('.')[:3])
  
  agaveapp = {
      'name': mriqc.__name__,
      'version': mriqc.__version__,
      'helpURI': 'http://mriqc.readthedocs.org',
      'label': 'mriqc',
      'shortDescription': mriqc.__description__,
      'longDescription': mriqc.__longdesc__,
      'executionSystem': 'slurm-stampede.tacc.utexas.edu',
      'executionType': 'HPC',
      'parallelism': 'PARALLEL',
      'defaultQueue': 'normal',
      'defaultNodeCount': 1,
      'deploymentPath': 'apps/mriqc',
      'deploymentSystem': 'openfmri-storage',
      'templatePath': 'wrapper.sh',
      'testPath': 'test/test.sh',
      'tags': ['qc', 'sMRI', 'fMRI'],
      'modules': [],
      'inputs': [{
          'id': 'bidsFolder',
          'details': {
              'label': 'folder',
              'description': 'input root folder of a BIDS-compliant tree',
              'argument': None,
              'showArgument': False
          },
          'value': {
              'visible': True,
              'required': True,
              'type': 'string'
          },
          'semantics': {
              'ontology': []
          }
      }],
      'parameters': [],
      'checkpointable': False
  }
  
  def main():
      """Entry point"""
  
      parser = ArgumentParser(description='ABIDE2BIDS downloader',
                              formatter_class=RawTextHelpFormatter)
  #    g_inputs = parser.add_argument_group('Inputs')
  #    g_inputs.add_argument('--help-uri', action='store')
  
      g_outputs = parser.add_argument_group('Outputs')
      g_outputs.add_argument('-o', '--output', action='store',
                             default='app.json')
  
      opts = parser.parse_args()
  
      with open(opts.output, 'w') as appfile:
          json.dump(agaveapp, appfile, indent=4)
  
  
  
  if __name__ == '__main__':
      main()
  
subject: fix version for agave