GenePattern MCP Server

Bridge any AI coding assistant directly to GenePattern — run bioinformatics modules, manage cloud jobs, and stream results, all through natural language.

→ genepattern/genepattern-mcp · listed on glama

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// key findings

✅

No credential exfiltration, no sensitive file access, no obfuscation

Static analysis found nothing flowing your secrets to unexpected places.

✅

Open source with a license and README

Anyone can audit the code, the license is declared, and the publisher documents what it does.

🔐

You'll be asked for 1 credential: GENEPATTERN_KEY

These are read from process.env at runtime. Make sure you trust where they’ll be sent.

// required environment variables

This server reads these from process.env. You'll be asked to provide them before it can run.

🔐 secretGENEPATTERN_KEY— export ="YOUR_TOKEN"

configGENEPATTERN_URL— e =https://cloud.genepattern.org/gp \

configLOCAL_FILES_ENABLED— local-files, -l True Enable local file upload/download tools

configAUTH_HANDLER— e =genepattern_mcp._shared.HeaderAuthHandler \

configFASTMCP_TRANSPORT— e =streamable-http \

configFASTMCP_PORT— port, -p 3000 Port to listen on (HTTP/SSE only)

configFASTMCP_HOST— e =0.0.0.0 \

// full audit trail

The full breakdown of what we checked, the deductions that landed, the network hosts, the dependency advisories, and concrete fix guidance is available to verified publishers.

// improvement guidance — verified publishers only

We have 4 concrete improvements we can share with the publisher of this MCP. Each comes with specific guidance to raise the trust score.

// embed badge in your README

[![M8ven Score](https://m8ven.ai/badge/mcp/genepattern-genepattern-mcp-1nomg7)](https://m8ven.ai/mcp/genepattern-genepattern-mcp-1nomg7)

commit: 0e81d31101f0362eb0e050b23408a2bec35da0bb

code hash: 43bfd904089abca0c4eb9ad9ebf9c50c0076db06afad64be30c87c4cfbfbccc3

verified: 6/23/2026, 10:08:03 AM

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