LPhyBEAST is a command-line program that takes a LPhy script file including model specification and data block, and produces a BEAST 2 XML file. It therefore enables LPhy as an alternative way to succinctly express and communicate BEAST2 analyses.
LPhyBEAST is implemented as an application in the BEAST 2 package "lphybeast".
But you need to add the extra repository
https://raw.githubusercontent.com/CompEvol/CBAN/master/packages-extra.xml
to the Package Manager to view it.
Follow the instruction to set up,
and then use the script lphybeast
to create the XML:
A simple usage of LPhyBEAST to create RSV2.xml
given
the LPhy script RSV2.lphy.
$BEAST_FOLDER/bin/lphybeast tutorials/RSV2.lphy
Create 10 BEAST 2 XMLs for a simple HKY+Coalescent simulation study:
$BEAST_FOLDER/bin/lphybeast -r 10 examples/hkyCoalescent
More scripts are available in linguaPhylo/examples.
LPhy and LPhyBEAST Tutorials
BEAST 2 packages, for example:
The details are in version.xml. All released BEAST 2 packages are listed in Package Viewer.
BEASTLabs beast.util.Script
depends on jdk.nashorn.api.scripting.ScriptObjectMirror
.
If there is NoClassDefFoundError
for it, you can add "-Xbootclasspath/a:${nashorn_path}" to your javac,
where ${nashorn_path}=/my/path/to/libext/nashorn.jar
.
More in another BEAST 2 package to host LPhyBeast extensions.