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 Poetry (Recommended)¶
poetry install
poetry shell
This installs all dependencies and makes the cde2linkml
command available in the poetry environment.
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¶
Read the Overview to understand the project
Explore Schema Documentation
Check out How-To Guides