NGS360 MCP Server

A Model Context Protocol (MCP) server that exposes the NGS360 REST API as tools for AI assistants.

Overview

This MCP server wraps the NGS360 bioinformatics platform API, providing tools for:

Related MCP server: openapi-mcp-bridge

Installation

cd mcp-server
pip install -e .

Or with uv:

cd mcp-server
uv pip install -e .

Configuration

The server uses environment variables for configuration:

Usage

Running directly

ngs360-mcp-server

With Claude Desktop

Add to your Claude Desktop configuration (~/Library/Application Support/Claude/claude_desktop_config.json):

{
  "mcpServers": {
    "ngs360": {
      "command": "ngs360-mcp-server",
      "env": {
        "NGS360_API_URL": "https://your-ngs360-api.example.com",
        "NGS360_API_TOKEN": "your-bearer-token",
      }
    }
  }
}

With VS Code / Roo

Add to your MCP settings:

{
  "mcpServers": {
    "ngs360": {
      "command": "ngs360-mcp-server",
      "env": {
        "NGS360_API_URL": "https://your-ngs360-api.example.com",
        "NGS360_API_TOKEN": "your-bearer-token",
      }
    }
  }
}

Development

Project Structure

mcp-server/
├── pyproject.toml
├── README.md
└── ngs360_mcp_server/
    ├── __init__.py
    ├── client.py          # HTTP client wrapper for the NGS360 API
    ├── server.py          # MCP server entry point
    └── tools/
        ├── __init__.py
        ├── runs.py        # Sequencing run tools
        ├── jobs.py        # Batch job tools
        ├── projects.py    # Project & sample tools
        ├── files.py       # File management tools
        ├── search.py      # Cross-index search tools
        ├── workflows.py   # Workflow management tools
        ├── pipelines.py   # Pipeline management tools
        ├── qcmetrics.py   # QC metrics tools
        ├── vendors.py     # Vendor management tools
        ├── settings.py    # Settings tools
        ├── platforms.py   # Platform registry tools
        ├── manifest.py    # Manifest tools

Testing with MCP Inspector

npx @modelcontextprotocol/inspector ngs360-mcp-server

Adding New Tools

1. Create or edit a file in ngs360_mcp_server/tools/

2. Define a register_*_tools(mcp, client) function

3. Register it in ngs360_mcp_server/server.py

Each tool is a decorated async function:

@mcp.tool()
async def my_new_tool(param1: str, param2: int = 10) -> dict:
    """Tool description shown to the AI assistant.

    Args:
        param1: Description of param1
        param2: Description of param2
    """
    return await client.get("/my/endpoint", params={"p": param1})

API Coverage

This MCP server covers the full NGS360 API surface at /api/v1/*:

• POST/GET /runs — Create and list sequencing runs

• GET/PUT /runs/{run_id} — Get/update a run

• GET /runs/{run_id}/samplesheet — Sample sheet

• GET /runs/{run_id}/metrics — Demux metrics

• GET/POST /runs/demultiplex — Demux workflows

• POST/GET/DELETE /runs/{run_id}/samples — Sample associations

• POST/GET /jobs — Submit and list batch jobs

• GET/PUT /jobs/{job_id} — Get/update job

• GET /jobs/{job_id}/log — Job logs

• POST/GET /projects — Create and list projects

• GET/PUT/PATCH /projects/{project_id} — Project CRUD

• POST/GET /projects/{project_id}/samples — Project samples

• POST /projects/{project_id}/actions/submit — Pipeline submission

• POST/GET /files — File record management

• GET/PATCH/DELETE /files/{file_id} — File operations

• GET /files/list — S3 browser

• GET /search — Global search

• POST/GET /workflows — Workflow identity

• POST/GET /workflows/{id}/versions — Versions

• PUT/GET/DELETE /workflows/{id}/aliases — Aliases

• POST/GET/DELETE /workflows/.../deployments — Deployments

• POST/GET /pipelines — Pipeline CRUD

• POST/DELETE /pipelines/{id}/workflows — Workflow membership

• POST/GET/DELETE /qcmetrics — QC records

• GET/POST /qcmetrics/search — QC search

• POST/GET/PUT/DELETE /vendors — Vendor management

• GET/PUT /settings — Application settings

• POST/GET /platforms — Platform registry

• GET/POST /manifest — Manifest operations

GA4GH WES API (/ga4gh/wes/v1/*)

• GET /service-info — WES service capabilities

• GET /runs — List workflow runs

• POST /runs — Submit a workflow run

• GET /runs/{run_id} — Full run log

• GET /runs/{run_id}/status — Run state

• POST /runs/{run_id}/cancel — Cancel a run

• GET /runs/{run_id}/tasks — List tasks for a run

• GET /runs/{run_id}/tasks/{task_id} — Get task details