Installation

Prerequisites

  • Python 3.9 or higher

  • Poetry (recommended) or pip

Installing from Source

Clone the repository:

git clone https://github.com/monarch-initiative/cde-harmonization.git
cd cde-harmonization

Using pip

pip install -e .

This installs the package in editable mode and creates the cde2linkml command.

Verifying Installation

Test the installation by running:

cde2linkml --help

You should see the command-line interface help message with options for --radx-up, --nih-nlm, and --phenx.

Dependencies

The project requires:

  • LinkML: Schema modeling framework

  • SSSOM: For mapping representations

  • Python packages: See pyproject.toml for full list

Data Access

Large data files are stored in the Monarch Google Cloud bucket. To access:

# Instructions for accessing cloud storage will be added

Development Installation

For development work, install with dev dependencies:

poetry install --with dev

This includes:

  • Testing frameworks (pytest)

  • Code formatting tools (black, ruff)

  • Documentation tools (sphinx)

Next Steps