What is sparrowhawk AGENTS.md?

Repository guidance for Sparrowhawk, a browser-based bioinformatics platform that runs Rust tools in the browser through WebAssembly, without uploading data to a server.

Use it when working on Sparrowhawk's Vue web app, Rust or WebAssembly tools, or repository setup. It covers the locations of tools such as sequence assembly, DNA mapping, taxonomic identification, and gene calling.

It helps coding agents get a working checkout and understand the project layout, renamed repositories, and facts that are easy to miss. It also points to the instructions for adding tools.

sparrowhawk AGENTS.md — Instructions file for Codex and OpenCode by bacpop: Repository guidance for Sparrowhawk, a browser-based bioinformat

Install

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.

agentmods

npx agentmods add instructions/bacpop/sparrowhawk/agents-md

Clone the repo

git clone --depth 1 https://github.com/bacpop/sparrowhawk

Made for: Codex, 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.

README.md

[![agentmods](https://agentmods.dev/badge/instructions/bacpop/sparrowhawk/agents-md.svg)](https://agentmods.dev/instructions/bacpop/sparrowhawk/agents-md)

Your own site

<a href="https://agentmods.dev/instructions/bacpop/sparrowhawk/agents-md"><img src="https://agentmods.dev/badge/instructions/bacpop/sparrowhawk/agents-md.svg" alt="Measured on agentmods" height="20"></a>

Per session 4,077 This file is loaded in full into every session.

When invoked 4,077 The same file — it is already loaded in full.

Security scan A 0 findings. Scan, not verified.

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.

Model	Per session	Once invoked
Fable 5	$0.04077	$0.04077
Opus 5	$0.02039	$0.02039
Sonnet 5	$0.00815	$0.00815
Haiku 4.5	$0.00408	$0.00408

Measured 4d ago against content hash 07d22de93fc4, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

sparrowhawk 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 4d 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.

AGENTS.md · 384 lines

How it starts

The opening of the file, as written. The whole thing — 384 lines — stays where its author put it; the contents beside it link to each section on GitHub.

AGENTS.md — sparrowhawk

Orientation for an AI agent working in this repository. Everything below was read from the tree on main; where something could not be verified it says so.

For how to add a new tool, read SKILLS.md — it is self-contained and needs neither this file nor the guide. docs/src/wasm_guide.md is the same WebAssembly material written for a human reader.

What this is

A browser-based bioinformatics platform. Rust crates compile to WebAssembly and run entirely client-side — no server, nothing uploaded. Each tool is a tab in a single Vue 3 SPA.

The repository was renamed: this is bacpop/sparrowhawk (formerly sparrowhawk-web), and the assembler crate is now bacpop/sparrowhawk-asm. Older checkouts and documents may still use the old names.

Eight tools, one page each under www/src/components/pages/:

Tool	Page	Crate
Assembly	`AssemblyPage.vue`	`sparrowhawk-asm`
Mapping / Alignment	`MappingAlignmentPage.vue`	`ska.rust`
Taxonomic ID	`TaxonomicIDPage.vue`	`sketchlib.rust`
Gene calling	`GeneCallingPage.vue`	`orphos-bridge`
Host depletion	`HostDepletionPage.vue`	`deacon-bridge`
AMR detection	`AMRDetectionPage.vue`	`sparrowhawk-amr`
Protein embeddings	`ProteinEmbeddingsPage.vue`	`esm-bridge`
Transmission	`TransmissionPage.vue`	(front-end analysis)

Plus FaqPage.vue.

Getting a working checkout

git clone --recurse-submodules https://github.com/bacpop/sparrowhawk.git
cd sparrowhawk/www && npm install && npm run serve

Without --recurse-submodules the rust/ submodule directories are empty and every wasm build fails. This is the most common way to arrive at a broken tree. Recover with git submodule update --init --recursive.

Requires the Rust toolchain plus wasm32-unknown-unknown, and wasm-pack.

Two facts that will otherwise cost you an hour

There is no hot reload. www/vue.config.js sets hot: false, liveReload: false and watchFiles: { paths: [] } deliberately — otherwise every file touch retriggers seven wasm-pack release builds. Restart npm run serve to see any change, front end included.
First start is slow. Seven crates compile in release mode before webpack runs.

Read the full file on GitHub · 384 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.

4d ago First seen · 384 lines · 4,077 tokens per session scan A 07d22de93fc4

Subscribe to this mod's changes

sparrowhawk AGENTS.md is an instructions file published in the GitHub repository bacpop/sparrowhawk (11 stars, last pushed 3d ago), licensed Apache-2.0. It adds 4,077 tokens to every session, about $0.0204 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 2026-08-30.

E-commerce

sparrowhawk AGENTS.md

Getting it into your agent

Wrote this? Show the measurements

What it costs to keep this loaded

Grade A, and why

Nothing flagged

How it starts

AGENTS.md — sparrowhawk

What this is

Getting a working checkout

Two facts that will otherwise cost you an hour

What this file has done since we first saw it

Other instructions, from other repositories

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