agentmods.dev

DNAnalyzer AGENTS.md

Repository instructions for DNAnalyzer, a Java and Spring Boot application with a command-line tool, a REST API, a web dashboard, and an optional Python DNA-alignment module.

In plain words
What is it for?
Use them when developing or verifying the Java application, REST endpoints, static dashboard, Docker setup, or Python analysis module.
Why use it?
They point agents to the authoritative architecture, repository map, API, and testing guidance before code is changed.

Instructions file for CodexOpenCode

185 4d ago A scan 1,306 tokens original MIT
View the source file VerisimilitudeX/DNAnalyzer
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/verisimilitudex/dnanalyzer/agents-md
Clone the repo
git clone --depth 1 https://github.com/VerisimilitudeX/DNAnalyzer

Made for: Codex, OpenCode.

Per session 1,306 This file is loaded in full into every session.
When invoked 1,306 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.

ModelPer sessionOnce invoked
Fable 5 $0.01306 $0.01306
Opus 5 $0.00653 $0.00653
Sonnet 5 $0.00261 $0.00261
Haiku 4.5 $0.00131 $0.00131

Measured yesterday against content hash 368de3803fff, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

DNAnalyzer 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 yesterday.

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 · 113 lines

How it starts

The opening of the file, as written. The whole thing — 113 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Agent Guide

This file is the entry point for agentic AI and automation tools. It tells an agent what the repository is, where things live, and how to make changes safely. Keep it short. Link out for detail.

What this repository is

DNAnalyzer is a Java 17 + Spring Boot 2.7 application with a static-HTML web dashboard and an optional Python Smith-Waterman module. It ships two interfaces on the same analysis core:

  1. CLI: DNAnalyzer.Main in src/main/java/DNAnalyzer/.
  2. REST API: DNAnalyzer.api.ApiApplication, mounted under /api/v1.

The org.openjfx.javafxplugin is still declared in build.gradle from an earlier GUI experiment, but no JavaFX source code is present.

The static frontend lives in web/. It is served by Nginx in the Docker stack and proxies /api/* to the Spring Boot container.

Canonical references for agents

Read these in order when you are new to the repo:

  1. README.md for the user-facing overview.
  2. docs/ARCHITECTURE.md for the system diagram and component responsibilities.
  3. docs/REPOSITORY_MAP.md for a directory-by- directory index.
  4. docs/API_REFERENCE.md for REST and CLI surface.
  5. docs/development/testing.md for how to run and extend tests.

If an agent makes changes that would invalidate any of the above, update that doc in the same change.

Build and verify

Always run the verification pipeline after a code change:

./gradlew test                     # Unit + integration tests (22 as of 2026-04)
./gradlew build -x test            # Produces build/libs/DNAnalyzer-<ver>-boot.jar
                                   # and DNAnalyzer-<ver>-plain.jar
docker compose config --quiet      # Validates docker-compose.yml

The bootJar has Start-Class: DNAnalyzer.api.ApiApplication. The plain jar has Main-Class: DNAnalyzer.Main (CLI). Do not confuse them.

Conventions that agents frequently get wrong

Read the full file on GitHub · 113 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. yesterday First seen · 113 lines · 1,306 tokens per session scan A 368de3803fff

Subscribe to this mod's changes

DNAnalyzer AGENTS.md is an instructions file published in the GitHub repository VerisimilitudeX/DNAnalyzer (185 stars, last pushed 4d ago), licensed MIT. It adds 1,306 tokens to every session, about $0.0065 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.

Analytics and metricsBackend and APIsDevOps and cloudartificial-intelligencebioinformaticsdna-sequencinggenomicsmachine-learningregulatory-elements
Related

Other instructions, from other repositories

marimo AGENTS.md

Instructions for marimo-team/marimo, covering marimo development guidelines, your primary responsibility is to the project and its users, quick setup, development commands and python.

marimo-team/marimo · 644 tokens

swarms CLAUDE.md

Instructions for kyegomez/swarms, covering claude.md — swarms framework guide, installation & setup, any provider supported by litellm works, project layout and core primitive: agent.

kyegomez/swarms · 8,544 tokens

marimo copilot-instructions.md

Instructions for marimo-team/marimo: For example, if there is a frontend change to make a border thicker, how does this look in run mode, app-view and edit-view? For a backend change, has the user tested different scenarios?

marimo-team/marimo · 91 tokens

spiceai copilot-instructions.md

Instructions for spiceai/spiceai, covering spice.ai agent instructions, data correctness — absolute top priority, evidence — no claim without a reproduction, build, test, lint (expensive — read first) and git & prs.

spiceai/spiceai · 7,971 tokens

spiceai AGENTS.md

Instructions for spiceai/spiceai, a project described as: Add a real-time analytics node to your operational database. Spice is a portable, accelerated SQL query, search, and LLM-inference engine in Rust for data-grounded AI apps and agents.

spiceai/spiceai · 6 tokens

texera AGENTS.md

Instructions for apache/texera, covering agents.md, architecture map, amber breakdown, where things live and agent-specific rules.

apache/texera · 3,084 tokens