Rbbt started as the Ruby Bioinformatics Toolkit.

Over time, many parts of “Rbbt core” were refactored into smaller, reusable libraries under the Scout umbrella. This makes it easier to:

• reuse the same core primitives in different projects
• keep configuration and prompts reproducible
• expose workflows as tools for agents
• support non-Ruby task implementations (notably Python)

A useful mental model:

• Rbbt is the user-facing framework + bioinformatics workflows ecosystem.
• Scout is the modern core library split that powers Rbbt.

Package map (where things live)

Area	What you get	Scout package(s)
Workflow engine	tasks, steps, dependencies, job directories, provenance/persistence	scout-gear
TSV / data tables	streaming TSV, semantics, indexing, traversal	scout-gear
Resources	bootstrapping data/software resources	scout-essentials
CMD / processes	running external tools, logging, streaming IO	scout-essentials
AI / chat files	endpoints, chat compilation, tool calling, agents	scout-ai
Python bridge	call Python from Ruby; pandas/TSV helpers; Python workflow client	scout-rig

Why the split matters for documentation

This documentation site keeps Rbbt as the front-door (the stable name many users search for), but increasingly documents features in “Scout terms”:

• because the newest capabilities land in Scout packages first
• because non-bioinformatics users may consume Scout directly

When a page says “Scout”, you can usually read it as “the modern core of Rbbt”.

How to proceed (practical guidance)

If you are a workflow user

Start with:

• Quickstart: run a workflow now
• Install & setup

If you are a workflow developer

Start with:

• Write workflows in Python (PythonWorkflow)
• Legacy deep dives:
  • Workflow tutorial
  • Resource tutorial

If you want the AI-native interface

Start with:

• Use workflows as tools for LLM agents

Notes on naming

You may encounter both rbbt and scout command names in different environments.

• Many deployments keep rbbt as the canonical CLI.
• Some Scout-only deployments use scout for framework-only usage.

This documentation tries to:

• use rbbt in Rbbt user-facing examples
• mention scout-ai explicitly for the AI tooling

See also:

• CLI overview (rbbt vs scout)
• AI section