Configuration Files

Included are sample configuration files; their names are of the form sample-X.ext where X is the configuration file name and ext is its extension. The program looks for a configuration file with the name X.ext in the same directory as the sample configuration file, so you can make a copy of the sample files and edit those as necessary.

config/db.cfg (Format: INI)

Section: database

host: The name of the host of the database (e.g., localhost)
dbname: The name of the database
user: The username to supply to access the database
password: The password to supply to access the database

config/codonpdx.cfg (Format: INI)

Section: refseq

pattern: Files to read when populating the refseq table
path: Path to local RefSeq release/complete directory

Section: genbank

pattern: Files to read when populating the genbank table
path: Path to local GenBank directory

Section: share

path: /path/to/www/pdxcodon/share/ (INSERT DESCRIPTION HERE)

config/mirror.cfg (Format: INI)

Section: genbank

local: Path to local directory to mirror GenBank into
remote: Remote location to mirror from

Section: refseq

local: Path to local directory to mirror RefSeq into
remote: Remote location to mirror from

codonpdx/celeryconfig.py (Format: Python)

This should be Python code that defines the following variables to configure Celery:

• BROKER_URL = 'amqp://localhost'
• CELERY_RESULT_BACKEND = 'amqp'
• CELERY_TASK_SERIALIZER = 'json'
• CELERY_RESULT_SERIALIZER = 'json'
• CELERY_ACCEPT_CONTENT = ['json']
• CELERY_TIMEZONE = 'US/Pacific'
• CELERY_ENABLE_UTC = True