samtools_faidx · Samtools MCP: Risk & Policy

WHAT IT DOES

What samtools_faidx does on Samtools

AI agents use samtools_faidx to create or update resources in Samtools — usually the action step of a workflow, after the agent has gathered context. Every call changes real data in your Samtools environment.

WHY IT NEEDS A POLICY

Why samtools_faidx needs a policy

This tool has dual functionality: (1) indexing FASTA files, which writes a new .fai index file to disk (a Write operation), and (2) extracting/reading sequences from an already-indexed FASTA (a Read operation). Since indexing creates a new file on disk, the most severe applicable category is Write. Misuse could overwrite existing index files, but data loss is unlikely since the original FASTA is not modified.

From the tool's definition Index FASTA files or extract sequences from indexed FASTA

Attacks that exploit this kind of access

Recommended rule Ready

Verdict

samtools_faidx Rate-limited

samtools_faidx stays usable, but capped — an agent stuck in a loop can't make hundreds of changes a minute. Everything else on the server is denied unless you say otherwise.

View as policy code

policy.json

{
  "version": "1",
  "default": "deny",
  "tools": {
    "samtools_faidx": {
      "limits": [
        {
          "counter": "samtools_faidx_rate",
          "window": "minute",
          "max": 30,
          "scope": "grant"
        }
      ]
    }
  }
}

LIMIT THIS TOOL →

Instant setup, no code required.

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

FAQ

Questions about samtools_faidx

What does the samtools_faidx tool do? +

Index FASTA files or extract sequences from indexed FASTA. It is categorised as a Write tool in the Samtools MCP Server, which means it can create or modify data. Consider rate limits to prevent runaway writes.

How do I enforce a policy on samtools_faidx? +

Register the Samtools MCP server in PolicyLayer and add a rule for samtools_faidx: 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 Samtools. Nothing to install.

What risk level is samtools_faidx? +

samtools_faidx is a Write tool with medium risk. Write tools should be rate-limited to prevent accidental bulk modifications.

Can I rate-limit samtools_faidx? +

Yes. Add a rate_limit block to the samtools_faidx 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 samtools_faidx completely? +

Set action: deny in the PolicyLayer policy for samtools_faidx. 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 samtools_faidx? +

samtools_faidx is provided by the Samtools MCP server (sirusb/samtools_mcp). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.