Installation

Runtime install

Install the package in editable mode for development:

pip install -e .[dev]

This installs the Python package and CLI entry point:

trait2gene --help

Documentation install

To build the Sphinx documentation locally:

pip install -e .[docs]
python scripts/build_sphinx_docs.py

Generated HTML is written to:

  • docs/build/html

External dependencies

trait2gene treats MAGMA as an external binary. It is not redistributed in the Python package. Depending on your run mode, you may also need local access to:

  • a PLINK reference panel prefix

  • a MAGMA gene location file

  • a PoPS gene annotation table

  • a pre-munged PoPS feature prefix or a raw feature directory

Public example without local MAGMA

The public schizophrenia tutorial uses:

  • resources.precomputed_magma_prefix

  • public raw feature files

That means you can run the end-to-end example without a local MAGMA install:

python scripts/run_public_schizophrenia_example.py