BeastFX

Applications for BEAST 2 with (most) GUIs based on Java FX.

Building & compiling

BEAST now uses Java 17 instead of Java 8, which might give a small performance boost for some models and allows access to Java 17 features.

It is recommended to install the JDK from Azul, since it allows painless integration of JavaFX. It can be downloaded from here: https://www.azul.com/downloads/?package=jdk

• scroll to the bottom
• select Java 17 LTS
• select your operating system
• select JDK FX ** make sure to include FX and not just select JDK without FX **
• download the file and install according to instructions under the How to install link.

In the IDE that you are using, make sure that the JDK points to Java 17.

It is convenient to make this JDK the default. For Linux, this can be done by adding to your ~/.bashrc file the following two lines:

export JAVA_HOME=/path/to/zulu17.34.19-ca-fx-jdk17.0.3-linux_x64 export PATH=${JAVA_HOME}/bin:${PATH}

Get code

BeastFX depends on BEAST 2, so make sure to clone both the BeastFX and BEAST 2 repository, e.g. like so:

git clone git@github.com:CompEvol/beast2.git git clone git@github.com:CompEvol/BeastFX.git

The build scripts assume beast2 and BeastFX have the same parent directory.

Include libraries

If you are using an IDE, make sure to include the following libraries from beast2/lib

• beagle.jar
  
• colt.jar
  
• commons-math3-3.6.1.jar
  
• antlr-runtime-4.10.1.jar
  
• junit/junit-platform-console-standalone-1.8.2.jar

and from BeastFX/locallib

• jam.jar -- gui library
• testfx.jar -- assists in testing
• FXSkins-1.0.0.jar -- GUI theme
• jmetro-11.6.15.jar -- GUI theme

Source folders

Sources are in BeastFX/src, and resources in BeastFX/resources.

If you are setting up in an IDE, make sure to include both as source folders, otherwise themes will not be available (i.e. dark mode will not work) when debugging.

Building from the command line

Use apache ant to build the BeastFX package.

ant package

should build the BEAST.app package in /path/to/BeastFX/build/dist/BEAST.base.package.v2.7.X.zip and /path/to/BeastFX/build/dist/BEAST.app.package.v2.7.X.zip where X the current version of BeastFX and /path/to/BeastFX the path to where BeastFX resides on your computer.

Releases containing all applications for your operating system can be built using one of:

• ant linux
• ant windows
• ant mac

This requires the jre for you operating system to be available, which can be downloaded from the Zulu website. Make sure that the openjreMac, openjreWnd or openjreLnx property at the top of the build.xml file in the BeastFX package points to where the JRE resides.