NGS360 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:

Domain	Tools	Description
Runs	14 tools	Sequencing run CRUD, sample sheets, metrics, demultiplexing
Jobs	6 tools	AWS Batch job submission, monitoring, and logs
Projects	11 tools	Project CRUD, samples, pipeline actions, vendor ingestion
Files	7 tools	File record management, S3 browsing
Search	1 tool	Cross-index search (projects, runs, samples)
Workflows	11 tools	Workflow identity, versions, aliases, deployments
Pipelines	5 tools	Pipeline CRUD, workflow associations
QC Metrics	5 tools	QC record creation, search, retrieval
Vendors	5 tools	Vendor CRUD
Settings	3 tools	Application settings management
Platforms	3 tools	Workflow execution platform registry
Manifest	2 tools	Manifest retrieval and validation
WES	8 tools	GA4GH Workflow Execution Service (run/monitor workflows)

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:

Variable	Default	Description
NGS360_API_URL	http://localhost:8000	Base URL of the NGS360 API
NGS360_API_TOKEN	(empty)	Bearer token for NGS360 authentication

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