Data Channels Configuration

Overview

Refgenieserver supports data channels - static files hosted by third-party providers that contain asset classes and recipes. Data channels are aggregated into a single unified interface, making it transparent to end users.

Configuration File

Create a data_channels.yaml file to configure multiple data channels:

data_channels.yaml

main:
  name: main
  protocol: https
  index_url: https://refgenie.github.io/recipes/index.yaml

custom_channel:
  name: custom_channel
  protocol: https
  index_url: https://example.com/my-recipes/index.yaml

dev:
  name: dev
  protocol: http
  index_url: http://localhost:8080/index.yaml

Configuration Parameters

• name: Channel identifier (cannot contain __ characters)
• protocol: http or https
• index_url: URL to the channel’s index.yaml file

Environment Configuration

Set the configuration file path via environment variable:

export DATA_CHANNELS_CONFIG_PATH="/path/to/your/data_channels.yaml"

Default location: refgenieserver/data_channels.yaml

Data Channel Format

Each data channel must expose an index.yaml file with this structure:

asset_class:
  dir: asset_classes
  files:
    - bowtie2_index_asset_class.yaml
    - bwa_index_asset_class.yaml
    - fasta_asset_class.yaml
recipe:
  dir: recipes
  files:
    - bowtie2_index_asset_recipe.yaml
    - bwa_index_asset_recipe.yaml
    - fasta_asset_recipe.yaml

API Endpoints

• GET /data_channels/ - List all configured channels
• GET /data_channels/index.yaml - Compiled index from all channels
• GET /data_channels/{channel_name}__{filename} - Access files from specific channels

How It Works

1. Refgenieserver loads all configured data channels at startup
2. Creates an aggregated index combining all channel files
3. Files are accessed using the format: {channel_name}__{filename}
4. Requests are transparently redirected to the appropriate data channel URL