demux_realm

demux_realm contains the active Yggdrasil realm for demultiplexing planning and pre-demux metadata preparation.

The realm currently:

• registers a ygg.realm entry point named dmx_realm;
• watches demux_sample_info and flowcell_status CouchDB changes;
• builds Yggdrasil plan drafts for flowcell-level initialization and lane-level demultiplexing work;
• prepares the pre-demux x_flowcells document from runfolder XML files, sample-sheet payloads, and uploaded LIMS metadata.

Setup

Create and activate a Python 3.11 environment:

conda create -n ygg python=3.11
conda activate ygg

Install Yggdrasil and this repository in editable mode:

git clone https://github.com/NationalGenomicsInfrastructure/Yggdrasil.git
pip install -e Yggdrasil

git clone https://github.com/NationalGenomicsInfrastructure/demux_realm.git
pip install -e demux_realm

Install local development dependencies:

pip install -e ".[dev]"

Yggdrasil is required to run the realm. It is kept out of the base install so the package can still be installed without fetching a Git dependency. When network and GitHub access are available, install Yggdrasil through the ygg extra:

pip install -e ".[ygg,dev]"

Yggdrasil Entry Point

On startup, Yggdrasil discovers the realm through pyproject.toml:

[project.entry-points."ygg.realm"]
dmx_realm = "demux_realm.descriptor:get_realm_descriptor"

The descriptor returns the dmx_realm realm with:

• DemuxHandler
• CouchDB watch specs for demux_sample_info_db
• CouchDB watch specs for flowcell_status_db

Repository Layout

demux_realm/
├── demux_realm/
│   ├── __init__.py
│   ├── descriptor.py
│   ├── handler.py
│   ├── recipes.py
│   ├── steps.py
│   └── utils.py
├── tests/
├── README.md
├── pyproject.toml
└── LICENSE

Development

Run the test suite:

pytest

Check that the package imports from the repository root:

python -c "import demux_realm; from demux_realm.descriptor import get_realm_descriptor"