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mutation-clinical-trial-matching-mcp: Instructions file for Claude Code

CLAUDE.md

mutation-clinical-trial-matching-mcp CLAUDE.md is an instructions file for Claude Code from pickleton89/mutation-clinical-trial-matching-mcp. It costs 2,331 tokens per session, scanned A, original, MIT.

A repository instruction file for a clinical-trial matching MCP project. It records commands for setup, dependency management, testing, and code quality checks using uv, a Python project tool.

In plain words
What is it for?
Use it when working on this repository to install dependencies, run unit or integration tests, measure coverage, and perform quality checks.
Why use it?
It gives coding agents the project's expected commands and conventions, reducing the chance of using the wrong environment or test process.

Instructions file for Claude Code

Written for Claude Code: the file is CLAUDE.md. Also seen: mentions CLAUDE.md; mentions Claude Code.

This is pickleton89/mutation-clinical-trial-matching-mcp's own configuration. It tells Claude Code how to work on mutation-clinical-trial-matching-mcp itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything mutation-clinical-trial-matching-mcp configures →

not rated 1repo 1y ago A scan 2,331 tokens original MIT
View source ↗ pickleton89/mutation-clinical-trial-matching-mcp
Reuse

Borrowing it

Nothing to install: this file belongs to pickleton89/mutation-clinical-trial-matching-mcp. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file
curl -O https://raw.githubusercontent.com/pickleton89/mutation-clinical-trial-matching-mcp/main/CLAUDE.md
Clone the repo
git clone --depth 1 https://github.com/pickleton89/mutation-clinical-trial-matching-mcp

Made for: Claude Code.

Wrote this? Show the measurements

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README.md
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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.

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<a href="https://agentmods.dev/instructions/pickleton89/mutation-clinical-trial-matching-mcp/claude-md"><img src="https://agentmods.dev/badge/instructions/pickleton89/mutation-clinical-trial-matching-mcp/claude-md.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 2,331 This file is loaded in full into every session.
When invoked 2,331 The same file — it is already loaded in full.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.02331 $0.02331
Opus 5 $0.01166 $0.01166
Sonnet 5 $0.00466 $0.00466
Haiku 4.5 $0.00233 $0.00233

Measured 10d ago against content hash c945a641ec58, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, from the pricing page.

Security

Grade A, and why

mutation-clinical-trial-matching-mcp CLAUDE.md 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 10d 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.

CLAUDE.md · 224 lines

How it starts

The opening of the file, as written. The whole thing — 224 lines — stays where its author put it; the contents beside it link to each section on GitHub.

CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Development Commands

Environment Setup

  • Package Manager: Always use uv for package management and environment setup
  • Sync Dependencies: uv sync (creates .venv and installs dependencies from uv.lock)
  • Add Dependencies: uv add <package> (adds to pyproject.toml and updates uv.lock)
  • Remove Dependencies: uv remove <package>
  • Run Commands: uv run <command> (runs command in project environment)

Testing

  • Run All Tests: uv run python -m unittest discover tests/
  • Run Specific Test: uv run python -m unittest tests.test_nodes.TestQueryTrialsNode.test_query_trials_node
  • Run with Pytest: uv run pytest (alternative test runner)
  • Test with Coverage: uv run pytest --cov
  • Test Files: Located in tests/ directory, following test_*.py pattern
  • Test Specific Components:
    • Unified nodes: uv run python -m unittest tests.test_unified_nodes
    • Legacy nodes: uv run python -m unittest tests.test_nodes
    • Server integration: uv run python -m unittest tests.test_unified_server

Code Quality

  • Linting: uv run ruff check (check for issues), uv run ruff format (auto-format code)
  • Type Checking: Install mypy with uv add --group dev mypy, then run uv run mypy .

MCP Server

  • Start Server: uv run python servers/main.py (recommended unified server)
  • Unified Server: servers/main.py (supports both sync and async modes)
  • Legacy Servers: servers/primary.py and servers/legacy/sync_server.py (deprecated, redirect to unified server)
  • Protocol: Uses FastMCP SDK for MCP protocol implementation
Unified Server Architecture (Phase 4 Complete)

The project has completed a major code deduplication effort, consolidating all server implementations:

  • servers/main.py: New unified server supporting both sync and async modes
  • Runtime Mode Selection: Automatic detection or explicit configuration via MCP_ASYNC_MODE
  • Backward Compatibility: Legacy servers still work but emit deprecation warnings
  • 60% Code Reduction: ~1,000 lines of duplicated code eliminated
  • Zero Breaking Changes: All existing APIs and configurations continue to work

Read the full file on GitHub · 224 lines

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. 10d ago First seen · 224 lines · 2,331 tokens per session scan A c945a641ec58

Subscribe to this mod's changes

mutation-clinical-trial-matching-mcp CLAUDE.md is an instructions file published in the GitHub repository pickleton89/mutation-clinical-trial-matching-mcp (1 stars, last pushed 1y ago), licensed MIT. It adds 2,331 tokens to every session, about $0.0117 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

Scientificagentic-codingai-assistantclaude-desktopclinicaltrialsgovgenetic-mutationmcp-server
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