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spatialtools

spatialtools is an MCP server for Claude Code, Codex, Cursor, Gemini CLI, OpenCode from lynnlangit/precision-medicine-mcp. Its token cost is not measured, scanned A, a copy of fgbio, Apache-2.0.

A local add-on that connects a coding agent to spatial data tools from the spatial-mcp Python package. It uses configured folders for data, cached files, and output, and is set to dry-run mode.

In plain words
What is it for?
Running spatial-data tasks that use files in the configured data folder and save results in the configured output folder. It is intended for local development and testing.
Why use it?
It gives the agent a defined way to work with spatial data on your computer without requiring a remote service. The available details do not specify which spatial operations it supports.

MCP server for Claude CodeCodexCursorGemini CLIOpenCode

Written for no agent in particular: it speaks MCP, so any client can run it. Also seen: listed in a Claude config.

Not installable: its command points at a path on the author’s own machine, so it runs nowhere else. The line is /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-spatialtools.

One of 19 entries in claude_desktop_config.json upstream. Installing this one merges just its entry into your config; the other 18 are separate, each on its own page.

not rated 24repo 16d ago A scan tokens not measured copy · 81% Apache-2.0

Good fit Running spatial-data tasks that use files in the configured data folder and save results in the configured output folder. It is intended for local development and testing.

Compare 6 mcp servers from other repositories ↓
View source ↗ lynnlangit/precision-medicine-mcp
Install

Getting it into your agent

There is no command for this one: it runs only inside a plugin, and the catalogue could not identify which plugin ships it. The source is linked below.

Made for: Claude Code, Codex, Cursor, Gemini CLI, OpenCode.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for spatialtools

README.md
[![agentmods](https://agentmods.dev/badge/mcp/lynnlangit/precision-medicine-mcp/desktop-configs-spatialtools/github.svg)](https://agentmods.dev/mcp/lynnlangit/precision-medicine-mcp/desktop-configs-spatialtools)
Your own site
<a href="https://agentmods.dev/mcp/lynnlangit/precision-medicine-mcp/desktop-configs-spatialtools"><img src="https://agentmods.dev/badge/mcp/lynnlangit/precision-medicine-mcp/desktop-configs-spatialtools/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for spatialtools

Your own site · 80×15
<a href="https://agentmods.dev/mcp/lynnlangit/precision-medicine-mcp/desktop-configs-spatialtools"><img src="https://agentmods.dev/badge/mcp/lynnlangit/precision-medicine-mcp/desktop-configs-spatialtools.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session not measured What this adds to a session before it is invoked.
When invoked not measured Not applicable: nothing here is loaded into a session.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin 81% copy Near-identical to another mod in the catalogue.
Security

Grade A, and why

spatialtools scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 11d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

Origin

This is a copy

81% identical to fgbio — 13 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.

docs/getting-started/desktop-configs/claude_desktop_config.json · 19 lines

What it actually says

{
  "spatialtools": {
    "command": "uv",
    "args": [
      "run",
      "--directory",
      "/Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-spatialtools",
      "python",
      "-m",
      "mcp_spatialtools"
    ],
    "env": {
      "SPATIAL_DATA_DIR": "/Users/lynnlangit/Documents/GitHub/spatial-mcp/data",
      "SPATIAL_CACHE_DIR": "/Users/lynnlangit/Documents/GitHub/spatial-mcp/data/cache",
      "SPATIAL_OUTPUT_DIR": "/Users/lynnlangit/Documents/GitHub/spatial-mcp/data/output",
      "SPATIAL_DRY_RUN": "true"
    }
  }
}
Same file

What else claude_desktop_config.json configures

This page is one entry in a file that holds 19. Installing the file brings all of them; each is measured and scanned on its own page.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 11d ago First seen · 19 lines scan A 3e4fe027bc04

Subscribe to this mod's changes

spatialtools is an MCP server published in the GitHub repository lynnlangit/precision-medicine-mcp (24 stars, last pushed 16d ago), licensed Apache-2.0. Its token cost is not measured: an MCP server costs its tool schemas, not its config file. A static security scan graded it A with 0 findings. It is 81% identical to fgbio, differing in 13 lines, and is treated as a copy.

Scientificagentic-aibioinformaticsmultiomicsprecision-medicinetranscriptomics
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