old_contents: import os
  import sys
  
  HOME=os.environ['HOME']
  LOGFILE = HOME+"/genenetwork2.log"
  
  # This is needed because Flask turns key errors into a
  # 400 bad request response with no exception/log
  TRAP_BAD_REQUEST_ERRORS = True
  
  DB_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s"
  SQLALCHEMY_DATABASE_URI = 'mysql://gn2:mysql_password@localhost/db_webqtl_s'
  
  # http://pythonhosted.org/Flask-Security/configuration.html
  SECURITY_CONFIRMABLE = True
  SECURITY_TRACKABLE = True
  SECURITY_REGISTERABLE = True
  SECURITY_RECOVERABLE = True
  SECURITY_EMAIL_SENDER = "no-reply@genenetwork.org"
  SECURITY_POST_LOGIN_VIEW = "/thank_you"
  SQLALCHEMY_POOL_RECYCLE = 3600
  
  SERVER_PORT = 5003
  SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a\xbc\xfc\x80:*\xebc'
  
  # Path overrides for Genenetwork
  GENENETWORK_FILES = HOME+"/gn2_data"
  PYLMM_COMMAND = str.strip(os.popen("which pylmm_redis").read())
  PLINK_COMMAND = str.strip(os.popen("which plink2").read())
  GEMMA_COMMAND = str.strip(os.popen("which gemma").read())
  
new_contents: import os
  import sys
  
  HOME=os.environ['HOME']
  LOGFILE = HOME+"/genenetwork2.log"
  
  # This is needed because Flask turns key errors into a
  # 400 bad request response with no exception/log
  TRAP_BAD_REQUEST_ERRORS = True
  
  DB_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s"
  SQLALCHEMY_DATABASE_URI = 'mysql://gn2:mysql_password@localhost/db_webqtl_s'
  
  # http://pythonhosted.org/Flask-Security/configuration.html
  SECURITY_CONFIRMABLE = True
  SECURITY_TRACKABLE = True
  SECURITY_REGISTERABLE = True
  SECURITY_RECOVERABLE = True
  SECURITY_EMAIL_SENDER = "no-reply@genenetwork.org"
  SECURITY_POST_LOGIN_VIEW = "/thank_you"
  SQLALCHEMY_POOL_RECYCLE = 3600
  
  SERVER_PORT = 5003
  SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a\xbc\xfc\x80:*\xebc'
  
  # Other settings (defaults)
  LOGGING        = WARNING        # Logger mode (DEBUG|INFO|WARNING|ERROR|CRITICAL)
  DEBUG_MODE     = 1              # Debug level (0-5)
  USE_REDIS      = True           # REDIS caching (redis will be phased out)
  
  # Path overrides for Genenetwork
  GENENETWORK_FILES = HOME+"/gn2_data"
  PYLMM_COMMAND = str.strip(os.popen("which pylmm_redis").read())
  PLINK_COMMAND = str.strip(os.popen("which plink2").read())
  GEMMA_COMMAND = str.strip(os.popen("which gemma").read())
  
subject: Add default settings