old_contents: import os
  import shutil
  import logging
  
  #try:
  #    from bcbio.install import _set_matplotlib_default_backend
  #    _set_matplotlib_default_backend()
  #except (ImportError, OSError, IOError):
  #    pass
  #import matplotlib
  #matplotlib.use('Agg', force=True)
  
  from libs.read import load_data
  from libs.report import make_profile
  from libs.utils import safe_dirs
  from db import make_database
  import templates
  
  logger = logging.getLogger('report')
  
  
  def report(args):
      """
      Create report in html format
      """
      logger.info("reading sequeces")
      data = load_data(args.json)
  
      logger.info("create profile")
      data = make_profile(data, out_dir, args)
      logger.info("create database")
      make_database(data, "seqcluster.db", args.out)
  
      logger.info("Done. Download https://github.com/lpantano/seqclusterViz/archive/master.zip to browse the output.")
  
new_contents: import os
  import shutil
  import logging
  
  #try:
  #    from bcbio.install import _set_matplotlib_default_backend
  #    _set_matplotlib_default_backend()
  #except (ImportError, OSError, IOError):
  #    pass
  #import matplotlib
  #matplotlib.use('Agg', force=True)
  
  from libs.read import load_data
  from libs.report import make_profile
  from libs.utils import safe_dirs
  from db import make_database
  import templates
  
  logger = logging.getLogger('report')
  
  
  def report(args):
      """
      Create report in html format
      """
      logger.info("reading sequeces")
      data = load_data(args.json)
  
      logger.info("create profile")
      data = make_profile(data, args.out, args)
      logger.info("create database")
      make_database(data, "seqcluster.db", args.out)
  
      logger.info("Done. Download https://github.com/lpantano/seqclusterViz/archive/master.zip to browse the output.")
  
subject: Fix out dir in report