Phenotype Database Configuration

The configuration file for a single phenotype database follows the general INI format. Its filename can be freely chosen, however, it must contain a phenoDB section - this will indicate that it is a phenotype database configuration file. This configuration file must properly describe a single phenotype database. Its properties, which must belong to the phenoDB section, are explained below.

Example Configuration

[phenoDB]
name = phenotypeDatabaseName
dbfile = %(wd)s/pheno.db
browser_dbfile = %(wd)s/browser/pheno_browser.db
browser_images_dir = %(wd)s/browser/images/
browser_images_url = /static/phenotypeDatabaseName/browser/images/

[phenoDB]

name

name = <pheno db name>

This is the unique name of the phenotype database. It can be used in the configuration files of studies and datasets to attach the phenotype database to them.

dbfile

dbfile = <sqlite3 pheno db path>

The path to the SQLite3 phenotype database file, relative to the configuration file.

browser_dbfile

browser_dbfile = <sqlite3 pheno browser db path>

The path to the SQLite3 phenotype browser database file, relative to the configuration file.

browser_images_dir

browser_images_dir = <images directory path>

The path to the directory containing the measure images for the browser, relative to the configuration file.

browser_images_url

browser_images_url = /static/<images directory path>/

The path to the directory containing the measure images for the browser, relative to the static root directory. The trailing slash is required.