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Installation

Requirements

  • Python 3.10 or later
  • For the build phase (create-db): 2–8 GB RAM per worker (see Performance Tuning)

pip

pip install afquery

To install the latest development version directly from GitHub:

pip install git+https://github.com/dlopez-bioinfo/afquery.git

conda / mamba (bioconda)

conda install bioconda::afquery

Or with mamba (faster):

mamba install bioconda::afquery

Docker

Official images are published to GitHub Container Registry for every release.

docker pull ghcr.io/dlopez-bioinfo/afquery:latest

Run the CLI by mounting a local directory with your database:

docker run --rm \
  -v /path/to/db:/db \
  ghcr.io/dlopez-bioinfo/afquery:latest \
  query --db /db --locus chr1:925952 --phenotype E11.9

Note

Images are available for linux/amd64 and linux/arm64. The latest tag always points to the most recent stable release.

From Source

git clone https://github.com/dlopez-bioinfo/afquery.git
cd afquery
pip install -e .

To also install documentation dependencies:

pip install -e ".[docs]"

Optional: Documentation Dependencies

If you want to build or serve the documentation locally:

pip install -e ".[docs]"
mkdocs serve

Next Steps