Borrowing it
Nothing to install: this file belongs to natecostello/genechat-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.
curl -O https://raw.githubusercontent.com/natecostello/genechat-mcp/main/CLAUDE.mdgit clone --depth 1 https://github.com/natecostello/genechat-mcpWrote 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.
[](https://agentmods.dev/instructions/natecostello/genechat-mcp/claude-md)<a href="https://agentmods.dev/instructions/natecostello/genechat-mcp/claude-md"><img src="https://agentmods.dev/badge/instructions/natecostello/genechat-mcp/claude-md/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.
<a href="https://agentmods.dev/instructions/natecostello/genechat-mcp/claude-md"><img src="https://agentmods.dev/badge/instructions/natecostello/genechat-mcp/claude-md.svg" alt="Reviewed on agentmods" width="80" height="20"></a>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.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.02756 | $0.02756 |
| Opus 5 | $0.01378 | $0.01378 |
| Sonnet 5 | $0.00551 | $0.00551 |
| Haiku 4.5 | $0.00276 | $0.00276 |
Grade A, and why
genechat-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 9d 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.
How it starts
The opening of the file, as written. The whole thing — 255 lines — stays where its author put it; the contents beside it link to each section on GitHub.
GeneChat MCP Server
PR Workflow
When submitting a PR, always request a GitHub Copilot review using:
gh pr edit <PR_NUMBER> --add-reviewer @copilot
Code Review
GitHub Copilot is configured as a PR code reviewer. Its instructions are in
.github/copilot-instructions.md. Copilot reviews
deliver inline comments with suggestion blocks. Use /resolve-pr-comments to process
review feedback.
Plan Compliance
When a PR implements a plan, the PR description MUST include a compliance section:
Plan Compliance
- Item 1: description -- DONE / DEVIATED / DEFERRED
- Item 2: description -- DONE / DEVIATED / DEFERRED ...
Each DEVIATED or DEFERRED item must include a one-line rationale.
Architecture Decision Records
ADRs live in docs/architecture/ using MADR 4.0 format with these project-specific additions:
When to write an ADR
Write an ADR when a decision:
- Changes how data flows between components (VCF, patch.db, lookup_tables.db, GWAS db)
- Affects the MCP tool interface (new tools, changed parameters, changed output format)
- Changes the annotation pipeline architecture (new sources, different processing)
- Affects module boundaries or adds/removes significant components
- Involves trade-offs between competing concerns that were debated
- Is hard to reverse once implemented
- Affects non-functional requirements (performance, security, privacy)
If in doubt, write the ADR — a short record is better than an undocumented decision.
Template conventions
- Frontmatter must include
status,date, andrelated ADRs(list of links to related ADRs in this directory). Optional fields:decision-makers,consulted,informed(per MADR 4.0 RACI convention) - Decision Drivers should capture the forces that shaped the decision
- Decision Outcome must reference the implementation plan with its file path and the git commit hash where the plan can be found (plans are deleted from the tree after implementation, but preserved in git history)
- Confirmation section should describe how compliance is verified (tests, code review, etc.)
- Pros and Cons of the Options — expand each option with bullet-point pros/cons, not just a one-line description
- More Information must list the PRs that implemented the decision (and the PR that removed legacy code, if applicable)
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.
- 9d ago First seen · 255 lines · 2,756 tokens per session scan A f0f0b08ffc86
genechat-mcp CLAUDE.md is an instructions file published in the GitHub repository natecostello/genechat-mcp (5 stars, last pushed 4mo ago), licensed MIT. It adds 2,756 tokens to every session, about $0.0138 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.
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