1 May 2023 by Remco Bouckaert

This post lists a few settings that can be passed to BEAST, BEAUti, etc. and change the behaviour of these programmes. They are mostly for developers. The way to use them is a java directives that can be passed to java using the -D argument, for example, use

$java -Dbeast.debug=true -cp launcher.jar beast.pkgmgmt.launcher.BeastLauncher beast.xml

to run BEAST with the beast.debug flag set to true.

In programs, these values can be obtained using

String property = System.getProperty(propertyName);

BEAST related

no.beast.popup

When BEAST starts, packages are loaded and package dependencies checked. If a dependency is missing, a warning is printed on screen notifying that the analysis may not run as expected.

prefix

Determines the prefix in the headers for LogAnalyser

beast.install.dir

Where the package manager should install packages.

beast.system.package.dir

Where system-wide packages can be found (defaults to \Program Files\BEAST2\2.7 on Windows, /Library/Application Support/BEAST2/2.7 on OS X and /usr/local/share/beast2/2.7 on Linux).

beast.user.package.dir

Where user installed packages can be found (defaults to \Users\<user name>\BEAST2\2.7 on Windows, ~/Library/Application Support/BEAST2/2.7 on OS X and ~/.beast/2.7 on Linux).

For developers, it can be useful to change this to a non-existing director to prevent any installed packaged to be loaded, so there is no interference from installed version of the package you are debugging.

BEAST_PACKAGE_PATH

The package path where the package manager first looks for packages. Can also be set as environment variable BEAST_PACKAGE_PATH.

beast.debug

If set to true, more debug information is produced, and more checks are done in the code. Can run less efficient because of these extra checks.

beast.instance.count

Number of instances that divide site patterns amongst number of threads used in threaded treelikelihoods. Can easier be set using the -instances option to BEAST.

beast.is.junit.testing

Flag to indicate a test is being run. This allows behaviour in test code to differ from regular running of the code.

beast.log.level

Determines the amount of logging and can have values error,warning,info,debug, and trace. Can easier be set using the -loglevel option to BEAST.

beast.resume

Flag to indicate we are resuming a BEAST run.

beast.useWindow

Flag to indicate BEAST is using a console window instead of terminal output.

file.name.prefix

Determines the prefix for the names of log files: will be pre-pended to each filename specified in Loggers. Can easier be set using the -prefix option to BEAST.

state.file.name

Determines the name of the state file to use. Can easier be set using the -statefile option to BEAST.

user.dir

Directory of last opened file. BEAST and BEAUti defaults to this directory when opening a file. Its value is stored in the beauti.properties file.

BEAGLE related

java.only

Do not use BEAGLE, but use the built-in java treelikelihood.

beagle.resource.order

Sets order of available BEAGLE resources to be used.

This is more conveniently set by the -beagle_order flag to BEAST.

beagle.preferred.flags

Flag to indicate which resource to use: CPU, SSE, GPU, etc. Also, which precision to use: single or double.

This is more conveniently set by the -beagle_CPU, -beagle_SSE, -beagle_GPU flag to BEAST as well as the -beagle_double and -beagle_single flags.

beagle.required.flags

Flag indicating requirements for BEAGLE, including whether the substitution model can return complex Eigen values and vectors.

beagle.scaling

Flag to set BEAGLE scaling: auto 1 « 6, none 1 « 7, always 1 « 8 or dynamic 1 « 19

Easier set via the -beagle_scaling flag for BEAST.

beagle.rescale

Frequency at which BEAGLE rescales when using dynamic scaling (10000 default).

Other directives

java.library.path

Library path used for loading system dependent libraries, like BEAGLE. Should be set together with the LD_LIBRARY_PATH environment variable to have effect. Setting one or the other may result in libraries not being loaded.

java.class.path

Path used for loading java libraries (jar files). Easier set through the -cp argument to java.

java.version

Java version.

os.name

Operating system name: Windows, Mac, Linux.

file.separator

Character used to separate files (“" or “/”).

path.separator

Character used to separate paths (“:” or “;”).

line.separator

Character used to separate lines.

user.home

User’s home directory – depends on operating system.