Developer Guide

This guide is for developers who want to build TASSEL from source, understand its internal architecture, add new analysis functionality, or contribute code back to the project.

TASSEL is written primarily in Java (with some Kotlin) and built with Gradle. The source lives on GitHub at maize-genetics/tassel.

Where to start

If you want to…	Read
Compile the code and produce a runnable sTASSEL.jar	Building from Source
Understand how the code is organized	Project Architecture
Add a new analysis, filter, or data operation	Developing Plugins
Run the test suite and check statistical correctness	Testing
Submit a change through a pull request	Contributing
Fix a typo or improve these docs	Documentation track
Cut a release and publish artifacts	Releasing

Branching model

TASSEL uses a develop integration branch: normal work flows feature/* -> develop -> main, and main holds released code. Branch off develop for your change (see Contributing); releases are promoted from develop to main (see Releasing). Documentation-only changes are the exception — they go straight to main and publish the site without cutting a release.

Toolchain at a glance

Tool	Version / Notes
Java (JDK)	21 — the build compiles to Java 21 bytecode via a Gradle toolchain
Kotlin	2.1.x (configured by the Gradle Kotlin plugin)
Build system	Gradle — use the bundled wrapper (./gradlew); no local install
Native BLAS	OpenBLAS (optional, recommended) for fast matrix operations
VCS	Git / GitHub
Recommended IDE	IntelliJ IDEA (imports the Gradle project directly)

Quick start

# Clone the repository
git clone https://github.com/maize-genetics/tassel.git
cd tassel

# Build the runnable JAR (output in build/libs/)
./gradlew build

# Launch the graphical interface
./gradlew run

See Building from Source for prerequisites (including OpenBLAS setup) and more detail.