Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add instructions/berntpopp/gencc-link/agents-mdgit clone --depth 1 https://github.com/berntpopp/gencc-linkWrote 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/berntpopp/gencc-link/agents-md)<a href="https://agentmods.dev/instructions/berntpopp/gencc-link/agents-md"><img src="https://agentmods.dev/badge/instructions/berntpopp/gencc-link/agents-md.svg" alt="Measured on agentmods" 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 | $0.01120 | $0.01120 |
| Opus 5 | $0.00560 | $0.00560 |
| Sonnet 5 | $0.00224 | $0.00224 |
| Haiku 4.5 | $0.00112 | $0.00112 |
Grade A, and why
gencc-link AGENTS.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 3d 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 — 99 lines — stays where its author put it; the contents beside it link to each section on GitHub.
AGENTS.md
Shared repository instructions for agentic coding tools working in GenCC-Link.
Project
GenCC-Link is a Python FastAPI + MCP server that grounds gene-disease validity questions in the Gene Curation Coalition (GenCC) dataset. GenCC harmonizes curated gene-disease assertions (Definitive ... Refuted) from member organizations (ClinGen, Genomics England PanelApp, Orphanet, Ambry, Invitae, Illumina, and others). GenCC has no live API yet, so the server downloads the bulk submissions export and serves it from a local SQLite + FTS5 database; the analytical value-add is per-pair consensus and conflict detection across submitters.
Primary areas:
gencc_link/- Python package: config, models, data store, services, MCP codeingest/- download + parse + build the SQLite databasedata/- schema.sql, read-only repository, repository Protocol (base.py)services/- consensus aggregation, response shaping, orchestrationmcp/- facade, tools, capabilities, envelope, next_commands, resources
tests/- unit and integration tests; fixtures undertests/fixtures/docker/- Dockerfile and Compose deployment filesdocs/- architecture, usage, and design specs (docs/superpowers/).claude/skills/- repo-local Claude Code workflows for recurring tasks
Source Of Truth
- Use this file for shared repo-wide agent guidance.
- Keep
CLAUDE.mdlean and Claude-specific; it should reference this file. - Prefer
Makefiletargets over ad hoc commands. - Use
uv.lockas the dependency lock source of truth. - The GenCC export schema and classification ranks live in
gencc_link/constants.py; the SQLite schema ingencc_link/data/schema.sql.
Working Rules
- Do not revert or overwrite changes you did not make unless explicitly asked.
- Keep edits scoped to the task and avoid unrelated refactors.
- Prefer existing code patterns over new abstractions.
- Put tests under
tests/; do not create alternate test roots. - Use ASCII unless a file already requires non-ASCII content.
- Keep public hosted MCP tools read-only and research-use scoped.
- Respect the GenCC download quota (20/IP/day): use HEAD + conditional requests (ETag / Last-Modified); never poll the full export in a loop.
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.
- 3d ago First seen · 99 lines · 1,120 tokens per session scan A 58657341f78f
gencc-link AGENTS.md is an instructions file published in the GitHub repository berntpopp/gencc-link (0 stars, last pushed today), licensed MIT. It adds 1,120 tokens to every session, about $0.0056 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.
Other instructions, from other repositories
genefoundry-router AGENTS.md
AGENTS.md instructions for berntpopp/genefoundry-router, covering agents.md, what this project is, required check before handoff, coding standards and project-specific guidance.
metadome-link AGENTS.md
AGENTS.md instructions for berntpopp/metadome-link, covering agents.md — metadome-link, what this is, two planes (non-negotiable boundary), async model and invariants.
metadome-link CLAUDE.md
Claude Code instructions for berntpopp/metadome-link, covering claude.md, essentials, common commands, fleet deploy contract and two-plane invariants (non-negotiable).
genefoundry-router CLAUDE.md
Claude Code instructions for berntpopp/genefoundry-router, a project described as: MCP gateway federating 21 biomedical MCP servers — gnomAD, ClinVar, HPO, UniProt, Ensembl VEP, PanelApp and more — behind one Streamable-HTTP endpoint, with collision-free namespaced tools and BM25 tool search.
biomed-agent AGENTS.md
Instructions for nickzren/biomed-agent, covering agent guide - biomed-agent, current direction, role, research contract and safety.
clingen-link AGENTS.md
AGENTS.md instructions for berntpopp/clingen-link, covering agents.md, project, source of truth, snapshot / refresh workflow and fleet deploy contract.