> For the complete documentation index, see [llms.txt](https://jfq3.gitbook.io/rdptools-docker/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://jfq3.gitbook.io/rdptools-docker/rdptools-docker/readme.md).

# RDPTools

RDPTools is a collection of command-line tools written by the RDP staff at Michigan State University and available at <https://github.com/rdpstaff/RDPTools>. Included are the well known RDP Classifier, Framebot for processing functional gene sequences and the gene targeted assembler Xander, as well as a variety of accesory utilities.

This document provides instructions for installing a Docker version of RDPTools on your computer. The steps are:

1. Install the Docker engine.
2. Create the RDP container.
3. Run a script to download and install auxillary third-party programs.


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter:

```
GET https://jfq3.gitbook.io/rdptools-docker/rdptools-docker/readme.md?ask=<question>&goal=<endgoal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.
