# For leadership: what this is and why it matters

> **In one sentence:** this project automates the tedious, error-prone upkeep of
> Galaxy's analysis tools, so scientists and maintainers spend less time on
> housekeeping and more on science, and so the tools stay correct and reproducible.

```mermaid
flowchart LR
    A[("Thousands of<br/>Galaxy tools")] --> B["Automated upkeep<br/>tidy · update · check"]
    B --> C["Less volunteer time<br/>on housekeeping"]
    B --> D["Tools stay valid,<br/>current and consistent"]
    C --> G{{"Advancing Galaxy and<br/>reproducible science"}}
    D --> G

    classDef start fill:#f3f3f3,stroke:#777777;
    classDef work fill:#e8f0ff,stroke:#3b5b9a,stroke-width:2px;
    classDef outcome fill:#e7f6e7,stroke:#3c7d3c;
    classDef goal fill:#fff3da,stroke:#b3852a,stroke-width:2px;
    class A start;
    class B work;
    class C outcome;
    class D outcome;
    class G goal;
```

## The problem, plainly

Galaxy is how a huge community runs reproducible bioinformatics. Every analysis tool
in Galaxy is described by a small configuration file. There are **thousands** of them,
maintained by volunteers. These files drift: the platform evolves, conventions change,
and keeping every tool tidy, valid, and up to date is slow, manual, and easy to get
wrong. That maintenance burden falls on a small number of expert volunteers, and it
competes directly with their time for actual research.

## What this project does

It turns much of that upkeep into something a computer can do reliably:

- **Tidies** tool files into a single consistent style.
- **Updates** tools to keep pace with the platform, making only the changes it can
  verify are safe.
- **Checks** tools against community best practices and reports what's missing.

In practice that can be dramatic: in one real case it brought a tool written for a
**2018-era version of Galaxy up to the current (2026) platform in a single step**,
applying only the changes it could verify were safe.

It works the same way whether a person runs it at the command line or an **AI assistant**
runs it on their behalf, which means it can plug into modern, automated workflows.

It is **grounded in evidence**: its behaviour is tuned against a library of **9,373 real
Galaxy tools**, so its decisions reflect how tools are actually written, not assumptions.

## Why it matters

- **Maintainer time is the scarce resource.** Automating housekeeping returns expert
  volunteer hours to science.
- **Reproducibility depends on tool correctness.** Consistent, valid, current tools mean
  analyses behave the same way tomorrow as they do today, the core promise of Galaxy
  and of reproducible science.
- **It strengthens the Galaxy ecosystem** rather than competing with it: it's designed to
  complement the community's existing tooling (see [vs planemo](vs-planemo.md)).

## Honest about today vs. tomorrow

**Today, it really does** format, safely upgrade, and check individual tools, usable now
as a command-line tool, a software library, and a service that AI agents can call.

> **Where it's going.** Two pieces of larger-scale automation already exist as **working
> reference implementations**: a pass that works through an entire tool collection and
> applies only the fixes it can prove are safe, and a pre-merge check a repository could
> run on incoming changes. What is still ahead is the *adopted, hands-off* version, a
> system trusted to propose fixes across the community's repositories on its own, and
> assistance that helps streamline the community's tool-review process. Crucially, neither
> piece runs on any repository today: whether and how to adopt them is the community's
> decision, not ours.

<details>
<summary>One honest limit, in plain terms</summary>

When it "upgrades" a tool, it guarantees the result is still a *valid* tool. It does **not**
blindly promise the tool behaves identically afterward. It only makes behaviour-changing
edits when it can prove they're safe, and otherwise flags them for a human. That caution is
deliberate: it's what makes the automation trustworthy.
</details>

---

*Every capability above is tracked, with its evidence and maturity, in
[capabilities](capabilities.md).*