Installation¶

Complete installation options for ToolUniverse

This Tutorial covers all installation methods and environment setup options.

System Requirements¶

Python 3.10 or higher
uv package manager (recommended) or pip
Internet connection for API access
GPU for machine learning models (optional)
API keys for external services (optional)

Installation Methods¶

Choose the installation method that best fits your needs:

Install ToolUniverse using pip:

pip install tooluniverse

Install with Optional Dependencies (pip)

For enhanced functionality:

pip install tooluniverse[dev]
pip install tooluniverse[embedding]
pip install tooluniverse[all]

Verify Installation

import tooluniverse
print(f"ToolUniverse version: {tooluniverse.__version__}")
print("✅ Installation successful!")

Test MCP Server

tooluniverse-mcp --help

Best for: Contributors, custom modifications

Clone and Install from Source (Recommended with uv)

For development or custom modifications:

# Clone the repository
git clone https://github.com/mims-harvard/ToolUniverse.git

# Add all dependencies
uv sync

Alternative: Clone and Install from Source (pip)

For development or custom modifications:

# Clone the repository
git clone https://github.com/mims-harvard/ToolUniverse.git

# Install in editable mode
pip install -e .

# Install development dependencies
pip install -e .[dev]

# Auto-setup pre-commit hooks (recommended)
./setup_precommit.sh

Alternative: Development Setup with Virtual Environment (pip)

# Create virtual environment
python -m venv tooluniverse-env
source tooluniverse-env/bin/activate  # On Windows: tooluniverse-env\Scripts\activate

# Install in development mode
pip install -e .[dev]

# Auto-setup pre-commit hooks (recommended)
./setup_precommit.sh

Best for: Isolated environments, CI/CD

Docker Installation

Create a Dockerfile:

FROM python:3.10-slim

WORKDIR /app
COPY requirements.txt .
RUN pip install -r requirements.txt
RUN pip install tooluniverse

CMD ["python", "-m", "tooluniverse.smcp_server"]

Docker Compose

version: '3.8'
services:
  tooluniverse:
    build: .
    ports:
      - "8000:8000"
    environment:
      - OPENTARGETS_API_KEY=${OPENTARGETS_API_KEY}
      - NCBI_API_KEY=${NCBI_API_KEY}
    volumes:
      - ./data:/app/data

Environment Configuration¶

Environment Variables

Set up API keys for enhanced functionality:

# Optional API keys for better performance
# Required API Keys
USPTO_API_KEY=your_uspto_key_here
HF_TOKEN=your_huggingface_token_here
NVIDIA_API_KEY=your_nvidia_key_here

# MCP Server Hosts
USPTO_MCP_SERVER_HOST=full_url_of_uspto_mcp_server
BOLTZ_MCP_SERVER_HOST=full_url_of_boltz_mcp_server
TXAGENT_MCP_SERVER_HOST=full_url_of_txagent_mcp_server
EXPERT_FEEDBACK_MCP_SERVER_URL=http://localhost:9877

# Optional API Keys (for enhanced features)
OPENAI_API_KEY=your_openai_key_here
AZURE_OPENAI_API_KEY=your_azure_key_here
GEMINI_API_KEY=your_gemini_key_here
FDA_API_KEY=your_fda_key_here
OPENTARGETS_API_KEY=your_opentargets_key_here
NCBI_API_KEY=your_ncbi_key_here
SEMANTIC_SCHOLAR_API_KEY=your_semantic_scholar_key_here

# Additional Configuration
OPENAI_BASE_URL=https://api.openai.com/v1
AZURE_OPENAI_ENDPOINT=https://your-endpoint.openai.azure.com
AZURE_OPENAI_API_VERSION=version_of_your_azure_api

Dependencies¶

ToolUniverse automatically installs core dependencies.

Install additional features:

# Development tools (uv - recommended)
uv add "tooluniverse[dev]" --dev

# Embedding functionality (uv - recommended)
uv add "tooluniverse[embedding]" --dev

# All optional dependencies (uv - recommended)
uv add "tooluniverse[all]" --dev

# Alternative with pip
pip install tooluniverse[dev]
pip install tooluniverse[embedding]
pip install tooluniverse[all]

Verification¶

Verify your installation:

import tooluniverse
print(f"ToolUniverse version: {tooluniverse.__version__}")
print("✅ Installation successful!")

Test MCP Server:

# Test MCP server
tooluniverse-mcp --help

# Start MCP server
python -m tooluniverse.smcp_server

Test Basic Functionality:

from tooluniverse import ToolUniverse

# Initialize and test
tu = ToolUniverse()
tu.load_tools()
print(f"✅ Loaded {len(tu.all_tools)} tools successfully!")

Troubleshooting¶

ImportError: No module named ‘tooluniverse’:

# Check Python environment
which python
pip list | grep tooluniverse

# Reinstall if needed
pip uninstall tooluniverse
pip install tooluniverse

Permission Denied Errors:

# Use user installation (pip)
pip install --user tooluniverse

# Or use virtual environment (pip)
python -m venv venv
source venv/bin/activate
pip install tooluniverse

# Or use uv (recommended - handles permissions automatically)
uv add tooluniverse --dev

Getting Help

If you encounter issues:

Check the GitHub Issues
Review the documentation
Create a new issue with detailed error information
Include system information and error logs