awslabs.aws-healthomics-mcp-server
Level ALocalAn 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.
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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