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Biomni Environment Setup

This directory contains scripts and configuration files to set up a comprehensive bioinformatics environment with various tools and packages.

  1. Clone the repository:

    git clone https://github.com/snap-stanford/Biomni.git
cd Biomni/biomni_env

  2. Setting up the environment:

  • (a) If you want to use or try out the basic agent without the full E1 or install your own softwares, run the following script:
conda env create -f environment.yml
  • (b) If you want to use the full environment E1, run the setup script (this script takes > 10 hours to setup, and requires a disk of at least 30 GB quota). Follow the prompts to install the desired components.
bash setup.sh

If you already installed the base version, and just wants to add the additional packages in the new release, you can simply do:

bash new_software_v004.sh

Note: we have only tested this setup.sh script with Ubuntu 22.04, 64 bit.

  1. Lastly, to activate the biomni environment:
conda activate biomni_e1