old_contents: # Copyright 2007-2014 University Of Southern 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.
  
  __author__ = 'dcbriggs'
  
  import os
  import sys
  
  #
  # Set OS automatically.
  #
  
  
  OS_TYPE = 'MACOSX' if sys.platform.startswith('darwin') else 'LINUX'
  
  
  #
  # GTFAR Configuration
  #
  
  
  GTFAR_HOME = '/data/workspace/gtfar'
  
  GTFAR_BIN_DIR = os.path.join(GTFAR_HOME, 'bin')
  GTFAR_DATA_DIR = os.path.join(GTFAR_HOME, 'data')
  
  # The directory from which Pegasus workflow runs will be invoked
  GTFAR_STORAGE_DIR = os.path.join(GTFAR_DATA_DIR, 'runs')
  
  # Directory where GTFAR reference input files will be placed
  GTFAR_REF_DIR = os.path.join(GTFAR_DATA_DIR, 'reference')
  GTFAR_REF_GTF_DIR = os.path.join(GTFAR_REF_DIR, 'gtf')
  GTFAR_REF_GENOME_DIR = os.path.join(GTFAR_REF_DIR, 'genome')
  
  GTFAR_EXECUTION_SITE = 'condorpool'
  GTFAR_STAGING_SITE = 'local'
  GTFAR_STORAGE_SITE = GTFAR_STAGING_SITE
  
  
  # A Temporary directory to upload files into.
  UPLOAD_FOLDER = '/tmp'
  
  # Limit max file upload size to 5GB
  
  MAX_UPLOAD_SIZE = 5000000000
  
  # Split input files in splits of .75GB
  
  SPLIT_DIVISOR = 400000000
  
  
  #
  # Pegasus Configuration
  #
  
  
  PEGASUS_HOME = '/data/software/pegasus/default'
  
  
  #
  # Server Configuration
  #
  
  
  SERVER_HOST = '127.0.0.1'
  SERVER_PORT = 5000
  ENDPOINT = None
  
  
  #
  # Flask Configuration
  #
  
  
  DEBUG = False
  
  # Secret key to encrypt session data
  SECRET_KEY = os.urandom(24)
  
  # The URI of the database
  SQLALCHEMY_DATABASE_URI = 'mysql://gtfar_user:pegasus123@127.0.0.1:3306/gtfar'
  
  #
  # Flask Cache Configuration
  #
  
  CACHE_TYPE = 'simple'
  
  #
  # User Authentication
  #
  USERNAME = ''
  PASSWORD = ''
  
new_contents: # Copyright 2007-2014 University Of Southern 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.
  
  __author__ = 'dcbriggs'
  
  import os
  import sys
  
  #
  # Set OS automatically.
  #
  
  
  OS_TYPE = 'MACOSX' if sys.platform.startswith('darwin') else 'LINUX'
  
  
  #
  # GTFAR Configuration
  #
  
  
  GTFAR_HOME = '/data/workspace/gtfar'
  
  GTFAR_BIN_DIR = os.path.join(GTFAR_HOME, 'bin')
  GTFAR_DATA_DIR = os.path.join(GTFAR_HOME, 'data')
  
  # The directory from which Pegasus workflow runs will be invoked
  GTFAR_STORAGE_DIR = os.path.join(GTFAR_DATA_DIR, 'runs')
  
  # Directory where GTFAR reference input files will be placed
  GTFAR_SPECIES_DIR = os.path.join(GTFAR_DATA_DIR, 'species')
  
  GTFAR_EXECUTION_SITE = 'condorpool'
  GTFAR_STAGING_SITE = 'local'
  GTFAR_STORAGE_SITE = GTFAR_STAGING_SITE
  
  
  # A Temporary directory to upload files into.
  UPLOAD_FOLDER = '/tmp'
  
  # Limit max file upload size to 5GB
  
  MAX_UPLOAD_SIZE = 5000000000
  
  # Split input files in splits of .75GB
  
  SPLIT_DIVISOR = 400000000
  
  
  #
  # Pegasus Configuration
  #
  
  
  PEGASUS_HOME = '/data/software/pegasus/default'
  
  
  #
  # Server Configuration
  #
  
  
  SERVER_HOST = '127.0.0.1'
  SERVER_PORT = 5000
  ENDPOINT = None
  
  
  #
  # Flask Configuration
  #
  
  
  DEBUG = False
  
  # Secret key to encrypt session data
  SECRET_KEY = os.urandom(24)
  
  # The URI of the database
  SQLALCHEMY_DATABASE_URI = 'mysql://gtfar_user:pegasus123@127.0.0.1:3306/gtfar'
  
  #
  # Flask Cache Configuration
  #
  
  CACHE_TYPE = 'simple'
  
  #
  # User Authentication
  #
  USERNAME = ''
  PASSWORD = ''
  
subject: Remove constants for GTF and Genome and add const. for Species dir.