Packages (previously known as add-ons or plugins) can be installed through BEAUti or from the command line.
The easiest way to Manage packages and install/un-install them is to start up BEAUti and select the menu File/Manage Packages. A window pops up where you can select the add-ons in the list to (un)install.
In the example above, BDSKY, BEAST_CLASSIC, BEASTlabs, MODEL_SELECTION, RBS and SNAPP are installed, and the rest are not.
older versions of BEAST
In the example above, SNAPP and RB are installed, and the rest are not.
To see where add-ons are installed, click the button with question mark in the dialog’s right left corner. A new dialog is shown with the information where you can find add-ons. Different operating systems have different locations where the add-ons are installed. There is a local add-on directory and a system wide add-on directory. Add-ons installed through the AddOnManager dialog in BEAUti are saved in the user’s local add-on directory. To install in the system wide directory, just move the directory with the add-on to the system wide add-on directory OR use the command line version (see below).
For computers without GUI, like high performance clusters, add-ons can be managed through the command line. An application called ‘addonmanager’ is part of the Linux distribution of BEAST, and has the following options:
Usage: addonmanager [-list] [-add
] [-del ] [-useAppDir] [-dir ] [-help] -list List available add-ons -add Install the add-on -del Uninstall the add-on -useAppDir Use application (system wide) installation directory. Note this requires writing rights to the application directory. If not specified, the user's BEAST directory will be used. -dir Install/uninstall add-on in direcotry . This overrides the useAppDir option -help Show help
Examples: addonmanager -list addonmanager -add SNAPP addonmanager -useAppDir -add SNAPP addonmanager -del SNAPP
Alternatively the add-on manager can be launched as
java -cp beast.jar beast.util.AddOnManager
Install by hand
If for some reason you cannot install a package through BEAUti or the package manager, you can always install the package by hand. First, get the zip file you want to install. For example, to install the VSS package, download https://github.com/CompEvol/CBAN/releases/download/v2.1.2/VSS.addon.v1.0.0.zip. Then, create a VSS subdirectory
for Windows in Users
BEAST2.XVSS for Mac in /Users/ /Library/Application Support/BEAST/2.X/VSS for Linux /home/ /.beast/2.X/VSS
Next, unzip the file VSS.addon.v1.0.0.zip inside the VSS directory
To install packages you need internet access.
Some software prevents access to the internet by programs like BEAUti. In that case, either tell the software to grant access to BEAUti, or install packages by hand.