awslabs.aws-healthomics-mcp-server

Level ALocal

An AWS Labs Model Context Protocol (MCP) server for AWS HealthOmics

Overview

An MCP server that gives AI assistants natural-language access to AWS HealthOmics for genomic workflows. It creates, lints, and packages WDL, CWL, and Nextflow workflows; starts and monitors runs; analyzes performance and resource usage; diagnoses failures; and retrieves logs and CloudWatch metrics. It also searches genomics files across S3 and HealthOmics stores and manages run groups and caches.

⭐ 9.9kDevOps & DeploymentPythonRepo ↗Updated 2026-11-05

Installation

MCP client config (paste into mcp.json)

{
  "mcpServers": {
    "awslabs-mcp-src-aws-healthomics-mcp-server": {
      "command": "uvx",
      "args": [
        "awslabs.aws-healthomics-mcp-server@latest"
      ],
      "env": {
        "FASTMCP_LOG_LEVEL": "ERROR",
        "AWS_REGION": "us-east-1"
      }
    }
  }
}

Agent install prompt

Copy and paste into Cursor / Claude / other agents to install this MCP for you

Please read this MCP repository and install it into my current environment:
https://github.com/awslabs/mcp/tree/main/src/aws-healthomics-mcp-server

Known working client config (can write into mcp.json):
{
  "mcpServers": {
    "awslabs-mcp-src-aws-healthomics-mcp-server": {
      "command": "uvx",
      "args": [
        "awslabs.aws-healthomics-mcp-server@latest"
      ],
      "env": {
        "FASTMCP_LOG_LEVEL": "ERROR",
        "AWS_REGION": "us-east-1"
      }
    }
  }
}

Please: 1) check README for deps and env vars; 2) write config for my client; 3) if secrets are missing, tell me what to fill — do not invent values.

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