Installation

1. Install environment and DeepFRI

  1. Clone repo locally

bash
git clone https://github.com/bioinf-mcb/Metagenomic-DeepFRI --recursive
cd Metagenomic-DeepFRI

  1. Setup conda environment

bash
conda env create --name deepfri --file environment.yml
conda activate deepfri

  1. Install meta-DeepFRI

bash
pip install .

  1. Verify installation

bash
pytest
deepfri --help

2. Retrieve DeepFRI model weights

CPU weights

bash
wget https://users.flatironinstitute.org/~renfrew/DeepFRI_data/newest_trained_models.tar.gz
tar -xf newest_trained_models.tar.gz

GPU weights

bash
wget https://users.flatironinstitute.org/~renfrew/DeepFRI_data/trained_models.tar.gz
tar -xf trained_models.tar.gz

Attention: Using DeepFRI with GPU requires extra installation steps, described in section 4. GPU Setup of tensorfow installation guide.