run_millimap_tool · Millimap MCP: Risk & Policy

WHAT IT DOES

What run_millimap_tool does on Millimap

AI agents invoke run_millimap_tool to trigger actions in Millimap. What it does depends on the arguments the agent supplies, and its effects often reach beyond the immediate call — builds kicked off, notifications sent, workflows started.

WHY IT NEEDS A POLICY

Why run_millimap_tool needs a policy

Without a description, we infer intent from context: this appears to be a dispatcher or runner for MilliMap analyses. Given sibling tools that perform state-modifying operations (clustering, QC filtering, scoring) and the 'run_*' naming convention, this tool likely executes computational pipelines whose effects depend on arguments and cannot always be trivially reversed.

From the tool's definition Tool name 'run_millimap_tool' with empty description; sibling tools include 'run_clustering', 'apply_qc_filter', 'score_gene_signature', and 'annotate_cluster' which modify or compute analysis state.

Attacks that exploit this kind of access

Recommended rule Ready

Verdict

run_millimap_tool Rate-limited

run_millimap_tool stays usable, but rate-capped — a runaway agent can't fire it dozens of times a minute. Everything else on the server is denied unless you say otherwise.

View as policy code

policy.json

{
  "version": "1",
  "default": "deny",
  "tools": {
    "run_millimap_tool": {
      "limits": [
        {
          "counter": "run_millimap_tool_rate",
          "window": "minute",
          "max": 10,
          "scope": "grant"
        }
      ]
    }
  }
}

RATE-LIMIT THIS TOOL →

Instant setup, no code required.

PolicyLayer is an MCP gateway: every tool call is checked against your rule before it reaches Millimap, so you can run agents against it safely.

FAQ

Questions about run_millimap_tool

What does the run_millimap_tool tool do? +

run_millimap_tool. It is categorised as a Execute tool in the Millimap MCP Server, which means it can trigger actions or run processes. Use rate limits and argument validation.

How do I enforce a policy on run_millimap_tool? +

Register the Millimap MCP server in PolicyLayer and add a rule for run_millimap_tool: allow, deny, rate-limit, or require approval. Point your MCP client at the PolicyLayer proxy URL and the rule is enforced on every call, before it reaches Millimap. Nothing to install.

What risk level is run_millimap_tool? +

run_millimap_tool is a Execute tool with high risk. Execute tools should be rate-limited and have argument validation enabled.

Can I rate-limit run_millimap_tool? +

Yes. Add a rate_limit block to the run_millimap_tool rule in your PolicyLayer policy. For example, setting max: 10 and window: 60 limits the tool to 10 calls per minute. Rate limits are tracked per agent session and reset automatically.

How do I block run_millimap_tool completely? +

Set action: deny in the PolicyLayer policy for run_millimap_tool. The AI agent will receive a policy violation error and cannot call the tool. You can also include a reason field to explain why the tool is blocked.

What MCP server provides run_millimap_tool? +

run_millimap_tool is provided by the Millimap MCP server (milliomics/millimap-mcp). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.