# Configuration: Overview

NOTE

This documentation is a work in progress and is incomplete.

Please contact developers for more details.

# Contents

The following pages describe various configurable aspects of ELLA:

# Overview of config files

# Application configuration

The main configuration of the ELLA application (excluding any data that is imported into the database, such as user/user group specific settings; see Fixtures) is set in a YAML file given by the ELLA_CONFIG environment variable, e.g. /config/ella_config.yml. This can also be used to set defaults for various user group settings.

In the YAML file, you may use environment variables using YAML constructors, such as my_key: !env ENVIRONMENT_VARIABLE, or my_key: !env [ENVIRONMENT_VARIABLE, "default"]. Custom YAML constructors available are !env_bool, !env_int, !env_float, and !file (file path relative to ELLA root folder).

Options for various settings are described in the above referred pages. See also /example_config.yml for examples.

# Fixtures

Fixtures include any kind of configuration data that should be imported into the database. If you have followed the setup described in Data directory, the following files are located under /data/fixtures/:

File/subfolder Configuration of ... More info
users.json User details Users
usergroups.json User group specific gene panels, ACMG rules, import, UI User groups
filterconfigs.json Variant filters Filtering
genepanels/ Gene panels (transcripts, phenotypes, ...) Gene panels

Examples can be found in /src/vardb/testdata/.

# Source code

Some configuration that should usually not be changed is located in the source code. This includes:

File Configuration of ... More info
/src/api/config/config.py VEP and ClinVar related settings
/src/api/config/acmgconfig.py Definition of ACMG criteria and REQs ACMG descriptions
/src/rule_engine/mapping_rules.py Rules for suggested ACMG criteria and REQs ACMG rules engine
Last Updated: 1/27/2020, 11:07:15 AM