Installation

Conda / Mamba is recommended for installation.

Create a conda environment:

mamba create -n dem python=3.11
mamba activate dem

# Install PyTorch with CUDA support
mamba install pytorch torchvision torchaudio pytorch-cuda=12.4 -c pytorch -c nvidia

Install biodem from PyPI

pip install biodem

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We also provide a lightweight tool pregv for VCF & GFF file processing and SNP encoding, which is implemented in Rust. Click to download or install with:

Install pregv

# mamba activate dem
dem-install-pregv

You may need to deactivate and reactivate the conda environment after installation.

Test your installation with:

Test pregv installation

pregv --help