Installation

This guide will help you install MultiModulon and its dependencies.

Requirements

  • Python 3.10 or higher

  • CUDA-capable GPU

  • Docker

Installation

Create multimodulon env

# Conda
conda create -n multimodulon python=3.11
conda activate multimodulon

Install BLAST+ (Required for BBH generation)

conda install -c bioconda blast

Install PyTorch (Required for multi-view ICA)

# Install PyTorch with CUDA support
pip install torch==2.6.0 torchvision==0.21.0 torchaudio==2.6.0 --index-url https://download.pytorch.org/whl/cu124

# Install geotorch
pip install geotorch==0.3.0

Install MultiModulon using pip:

pip install git+https://github.com/Gaoyuan-Li/multimodulon.git

Development Installation

For development:

git clone https://github.com/yourusername/multimodulon.git
cd multimodulon
pip install -e .

Dependencies

Core dependencies will be automatically installed:

  • numpy

  • pandas

  • matplotlib

  • scikit-learn

  • pytorch (for robust multi-view ICA)

  • biopython (for sequence handling)

Verifying Installation

To verify that MultiModulon is installed correctly:

import multimodulon
print(multimodulon.__version__)