# 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:
- Application
- Users and user groups
- User interface
- Annotation
- Gene panels
- Import and deposit
- Filtering
- ACMG and classification
# 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. /data/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 (opens new window) 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 alleles/ella-testdata (opens new window).
# 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 |