Building from Source¶

TASSEL is built with Gradle. A Gradle wrapper (./gradlew) is committed to the repository, so you do not need a local Gradle installation — the wrapper downloads the correct version automatically.

Prerequisites¶

Requirement	Details
Java 21 (JDK)	The build uses a Gradle toolchain targeting Java 21 and compiles to Java 21 bytecode. Verify with `java -version`.
Git	Needed to clone the repository. Verify with `git --version`.
OpenBLAS (optional, recommended)	A native BLAS library that accelerates matrix operations and is required by some statistical tests.

Installing OpenBLAS¶

Some analyses (kinship, MLM, PCA, and the statistical test suite) call into a native BLAS library through JNI. Installing OpenBLAS is optional for a plain build, but recommended for full functionality and required to run the statistics test gate.

macOSLinux (Debian/Ubuntu)

brew install openblas

sudo apt-get update
sudo apt-get install -y libopenblas-dev

The build and test tasks auto-detect common install locations (/opt/homebrew/opt/openblas/lib and /usr/local/opt/openblas/lib on macOS, /usr/lib/x86_64-linux-gnu on Linux). If your library lives elsewhere, point at it with the BLAS_LIB_PATH environment variable:

export BLAS_LIB_PATH=/path/to/dir/containing/libopenblas

Getting the source¶

git clone https://github.com/maize-genetics/tassel.git
cd tassel

To update an existing checkout to the latest code:

git pull

Building¶

Build the project and assemble the runnable JAR:

./gradlew build

This produces:

build/libs/sTASSEL.jar — the TASSEL application JAR. Its manifest declares the main class and a Class-Path that points at lib/.
build/libs/lib/ — all runtime dependencies, copied next to the JAR so the manifest classpath resolves.

A self-contained JAR that needs no lib/ directory is available too, but it is built only on demand because it is over 70 MB:

./gradlew shadowJar   # build/libs/tassel-<version>-jar-with-dependencies.jar

To do a clean rebuild:

./gradlew clean build

Skipping tests during a build

The full build runs the enforced statisticsTest gate (wired into check). To build the JAR without running tests — for example, when you just need an artifact quickly — skip the test tasks:

./gradlew clean build -x test -x statisticsTest

Running¶

Graphical interface¶

Run through Gradle:

./gradlew run

Or launch the built JAR directly (the manifest supplies the main class and classpath):

java -jar build/libs/sTASSEL.jar

Command-line pipeline¶

TASSEL analyses can be scripted through the pipeline entry point, net.maizegenetics.pipeline.TasselPipeline:

java -classpath 'build/libs/sTASSEL.jar:build/libs/lib/*' \
  net.maizegenetics.pipeline.TasselPipeline -h

Increase the heap for large datasets with a -Xmx flag, e.g. -Xmx10g. For the full pipeline command language, see the TASSEL 5 Pipeline (CLI) documentation.

Useful Gradle tasks¶

Task	Purpose
`./gradlew build`	Compile, test, and assemble `sTASSEL.jar` + `lib/`.
`./gradlew run`	Launch the Swing GUI.
`./gradlew test`	Run the full (non-blocking) test suite.
`./gradlew statisticsTest`	Run the enforced statistical-correctness gate.
`./gradlew koverHtmlReport`	Generate an HTML code-coverage report.
`./gradlew dokkaGenerate`	Generate API documentation with Dokka.
`./gradlew shadowJar`	Assemble the self-contained `jar-with-dependencies` JAR.
`./gradlew fetchTestData`	Download the shared test-data archive into `dataFiles/`.
`./gradlew printVersion`	Print the current project version.

Run ./gradlew tasks to see the full list.

Common issues¶

UnsatisfiedLinkError / BLAS failures — OpenBLAS is not installed or not found. Install it (see above) or set BLAS_LIB_PATH.
Wrong Java version — the toolchain targets Java 21. Make sure a JDK 21 is installed and discoverable; Gradle can auto-provision a toolchain, but a local JDK 21 avoids surprises.
Out-of-memory during large analyses — increase the JVM heap with -Xmx.