old_contents: # Copyright (C) 2015-2016 Regents of the University of California
  #
  # Licensed under the Apache License, Version 2.0 (the "License");
  # you may not use this file except in compliance with the License.
  # You may obtain a copy of the License at
  #
  #     http://www.apache.org/licenses/LICENSE-2.0
  #
  # Unless required by applicable law or agreed to in writing, software
  # distributed under the License is distributed on an "AS IS" BASIS,
  # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  # See the License for the specific language governing permissions and
  # limitations under the License.
  
  """Kills any running jobs trees in a rogue toil.
  """
  from __future__ import absolute_import
  import logging
  
  from toil.lib.bioio import getBasicOptionParser
  from toil.lib.bioio import parseBasicOptions
  from toil.common import Toil, jobStoreLocatorHelp, Config
  from toil.version import version
  
  logger = logging.getLogger( __name__ )
  
  def main():
      parser = getBasicOptionParser()
  
      parser.add_argument("jobStore", type=str,
                          help="The location of the job store used by the workflow whose jobs should "
                               "be killed." + jobStoreLocatorHelp)
      parser.add_argument("--version", action='version', version=version)
      options = parseBasicOptions(parser)
      config = Config()
      config.setOptions(options)
      jobStore = Toil.resumeJobStore(config.jobStore)
  
      logger.debug("Starting routine to kill running jobs in the toil workflow: %s", config.jobStore)
      ####This behaviour is now broken
      batchSystem = Toil.createBatchSystem(jobStore.config) #This should automatically kill the existing jobs.. so we're good.
      for jobID in batchSystem.getIssuedBatchJobIDs(): #Just in case we do it again.
          batchSystem.killBatchJobs(jobID)
      logger.debug("All jobs SHOULD have been killed")
  
new_contents: # Copyright (C) 2015-2016 Regents of the University of California
  #
  # Licensed under the Apache License, Version 2.0 (the "License");
  # you may not use this file except in compliance with the License.
  # You may obtain a copy of the License at
  #
  #     http://www.apache.org/licenses/LICENSE-2.0
  #
  # Unless required by applicable law or agreed to in writing, software
  # distributed under the License is distributed on an "AS IS" BASIS,
  # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  # See the License for the specific language governing permissions and
  # limitations under the License.
  
  """Kills any running jobs trees in a rogue toil.
  """
  from __future__ import absolute_import
  import logging
  
  from toil.lib.bioio import getBasicOptionParser
  from toil.lib.bioio import parseBasicOptions
  from toil.common import Toil, jobStoreLocatorHelp, Config
  from toil.version import version
  
  logger = logging.getLogger( __name__ )
  
  def main():
      parser = getBasicOptionParser()
  
      parser.add_argument("jobStore", type=str,
                          help="The location of the job store used by the workflow whose jobs should "
                               "be killed." + jobStoreLocatorHelp)
      parser.add_argument("--version", action='version', version=version)
      options = parseBasicOptions(parser)
      config = Config()
      config.setOptions(options)
      jobStore = Toil.resumeJobStore(config.jobStore)
  
      logger.info("Starting routine to kill running jobs in the toil workflow: %s", config.jobStore)
      ####This behaviour is now broken
      batchSystem = Toil.createBatchSystem(jobStore.config) #This should automatically kill the existing jobs.. so we're good.
      for jobID in batchSystem.getIssuedBatchJobIDs(): #Just in case we do it again.
          batchSystem.killBatchJobs(jobID)
      logger.info("All jobs SHOULD have been killed")
  
subject: Change logging around killing jobs to be INFO