Installation & Setup

Get OmicsAgent.ai running in under 10 minutes. All 15 skills work with no API key needed for demo mode.

Prerequisites

Option A — Conda (recommended)

conda create -n omicsagent python=3.11 -y
conda activate omicsagent
git clone https://github.com/madhubioinformatics/OmicsAgent
cd OmicsAgent
pip install -r requirements.txt

Option B — pip + venv

python3 -m venv .venv && source .venv/bin/activate
git clone https://github.com/madhubioinformatics/OmicsAgent
cd OmicsAgent
pip install -r requirements.txt

Option C — Docker

docker pull madhubioinformatics/omicsagent:latest
docker run -e ANTHROPIC_API_KEY=$ANTHROPIC_API_KEY \
  madhubioinformatics/omicsagent python3 omics_agent.py --demo

Set API Key

# Temporary (current session)
export ANTHROPIC_API_KEY="sk-ant-api03-..."

# Permanent (.env file)
echo 'ANTHROPIC_API_KEY=sk-ant-api03-...' > .env

Verify Installation

python3 omics_agent.py --list

# Expected output:
  o  genomics           Genomics (WGS/WES/SNP)
  o  scrna              scRNA-seq (Single-cell)
  o  scatac             scATAC-seq (ChromVAR / LSI)
  o  spatial_full       Spatial (Visium/MERFISH/CosMx/Stereo-seq)
  o  scTCR_BCR          scTCR/BCR-seq (Immune Repertoire)
  ... 10 more skills

Next Steps