iflow-mcp_galaxyproject-galaxy-mcp 1.3.0
Model Context Protocol server for Galaxy bioinformatics platform
Requires Python: >=3.10

# Galaxy MCP Server - Python Implementation

<!-- mcp-name: io.github.galaxyproject/galaxy-mcp -->

This is the Python implementation of the Galaxy MCP server, providing a Model Context Protocol server for interacting with Galaxy instances.

## Features

- Complete Galaxy API integration through BioBlend
- Optional OAuth login flow for HTTP deployments
- Interactive Workflow Composer (IWC) integration
- FastMCP2 server with remote deployment support
- Type-annotated Python codebase

## Requirements

- Python 3.10+
- FastMCP 2.3.0+

## Installation

### From PyPI (Recommended)

```bash
# Install from PyPI
pip install galaxy-mcp

# Or using uv (recommended)
uvx galaxy-mcp
```

### From Source

```bash
# Clone the repository
git clone https://github.com/galaxyproject/galaxy-mcp.git
cd galaxy-mcp/mcp-server-galaxy-py

# Install with uv (recommended)
uv sync --all-extras
```

## Configuration

At minimum the server needs to know which Galaxy instance to target:

```bash
export GALAXY_URL="https://usegalaxy.org.au/"
```

How you authenticate depends on your transport:

- **Stdio / long-lived sessions** – provide an API key:

  ```bash
  export GALAXY_API_KEY="your-api-key"
  ```

- **HTTP / OAuth** – configure the public URL that users reach and a signing secret for session
  tokens. The server mints short-lived Galaxy API keys on behalf of each user.

  ```bash
  export GALAXY_MCP_PUBLIC_URL="https://mcp.example.com"
  export GALAXY_MCP_SESSION_SECRET="$(openssl rand -hex 32)"
  ```

  Optionally set `GALAXY_MCP_CLIENT_REGISTRY` to control where OAuth client registrations are stored.

You can also steer the transport with `GALAXY_MCP_TRANSPORT` (`stdio`, `streamable-http`, or `sse`).
All variables can be placed in a `.env` file for convenience.

## Usage

### Quick Start with `uvx`

```bash
# Local stdio transport (no network listener)
uvx galaxy-mcp

# Remote/browser clients with HTTP + OAuth
export GALAXY_URL="https://usegalaxy.org.au/"
export GALAXY_MCP_PUBLIC_URL="https://mcp.example.com"
export GALAXY_MCP_SESSION_SECRET="$(openssl rand -hex 32)"
uvx galaxy-mcp --transport streamable-http --host 0.0.0.0 --port 8000
```

### Installed CLI

```bash
pip install galaxy-mcp
galaxy-mcp --transport streamable-http --host 0.0.0.0 --port 8000
```

If `--transport` is omitted the server defaults to stdio and reads/writes MCP messages via stdin/stdout.

### Working from a checkout

```bash
uv sync
uv run galaxy-mcp --transport streamable-http --host 0.0.0.0 --port 8000
```

See [USAGE_EXAMPLES.md](USAGE_EXAMPLES.md) for detailed tool usage patterns.

## Available MCP Tools

The Python implementation provides the following MCP tools:

- `connect`: Establish connection to a Galaxy instance
- `search_tools_by_name`: Find Galaxy tools by name
- `get_tool_details`: Retrieve detailed tool information
- `run_tool`: Execute a Galaxy tool with parameters
- `get_tool_panel`: Retrieve the Galaxy tool panel structure
- `get_tool_run_examples`: Retrieve XML-defined test lessons that show how to run a tool
- `get_user`: Get current user information
- `get_histories`: List available Galaxy histories
- `list_history_ids`: Get simplified list of history IDs and names
- `get_history_details`: Get detailed information about a specific history
- `upload_file`: Upload local files to Galaxy
- `upload_file_from_url`: Upload files from URLs to Galaxy
- `list_workflows`: List available workflows in Galaxy instance
- `get_workflow_details`: Get detailed information about a specific workflow
- `invoke_workflow`: Execute/run a workflow with specified inputs
- `cancel_workflow_invocation`: Cancel a running workflow invocation
- `get_invocations`: View workflow executions
- `get_iwc_workflows`: Access Interactive Workflow Composer workflows
- `search_iwc_workflows`: Search IWC workflows by keywords
- `import_workflow_from_iwc`: Import an IWC workflow to Galaxy

## Testing

The project includes a comprehensive test suite using pytest with mock-based testing.

### Running Tests

```bash
# Install test dependencies
uv pip install -r requirements-test.txt

# Run all tests
uv run pytest

# Run with coverage report
uv run pytest --cov=main --cov-report=html

# Run specific test file
uv run pytest tests/test_history_operations.py

# Run tests with verbose output
uv run pytest -v
```

### Test Structure

Tests are organized by functionality:

- `test_connection.py` - Galaxy connection and authentication
- `test_history_operations.py` - History-related operations
- `test_dataset_operations.py` - Dataset upload/download
- `test_tool_operations.py` - Tool search and execution
- `test_workflow_operations.py` - Workflow import and invocation
- `test_integration.py` - End-to-end scenarios

See [tests/README.md](tests/README.md) for more details on the testing strategy.

## Development

### Code Style Guidelines

- Use Python 3.10+ features
- Employ type hints where appropriate
- Follow PEP 8 style guidelines
- Use ruff for code formatting and linting
- All code should pass type checking with mypy

### Development Setup

```bash
# Install development dependencies
make install-dev

# Set up pre-commit hooks (required for contributing)
uv run pre-commit install
```

Pre-commit hooks will automatically format your code and run linting checks when you commit. All contributors should install these hooks to maintain consistent code quality.

### Development Commands

We use a Makefile for consistent development commands:

```bash
# Show all available commands
make help

# Install dependencies
make install       # Install all dependencies

# Code quality
make lint          # Format code and run all checks

# Testing
make test          # Run tests with coverage

# Building
make clean         # Clean build artifacts
make build         # Build distribution packages

# Running
make run           # Run the MCP server
make dev           # Run FastMCP2 dev server
```

### Using uv directly

All commands can also be run directly with uv:

```bash
# Install dependencies
uv sync --all-extras

# Format and lint code
uv run pre-commit run --all-files

# Run tests with coverage
uv run pytest --cov=galaxy_mcp --cov-report=html

# Update dependencies
uv lock --upgrade
```

### Cross-version Testing

Test across multiple Python versions using tox:

```bash
# Test on all supported Python versions
tox

# Test on specific version
tox -e py312

# Run only linting
tox -e lint

# Run type checking
tox -e type
```

### Pre-commit Hooks

The project uses pre-commit hooks for automatic code quality checks:

```bash
# Install pre-commit hooks (one-time setup)
uv run pre-commit install

# Run pre-commit manually on all files
uv run pre-commit run --all-files

# Skip pre-commit for a single commit (not recommended)
git commit --no-verify
```

Pre-commit runs automatically on `git commit` and includes:

- Code formatting with ruff
- Linting with ruff
- Trailing whitespace removal
- File cleanup (EOF, YAML/JSON/TOML validation)
- Large file detection
- Merge conflict detection

## License

[MIT](../LICENSE)