BEAST 2

Managing Packages

Packages (previously known as add-ons or plugins) can be installed through BEAUti or from the command line.

Desktop machines

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 packages in the list to (un)install.

Package_manager

BEAST 2.1.2

In the example above, BDSKY, BEAST_CLASSIC, BEASTlabs, MODEL_SELECTION, RBS and SNAPP are installed, and the rest are not.

AddOnManagerDialog

older versions of BEAST

In the example above, SNAPP and RB are installed, and the rest are not.

Installation directories

To see where packages 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 packages. Different operating systems have different locations where the packages are installed. There is a local package directory and a system wide package directory. Packages installed through the packagemanager dialog in BEAUti are saved in the user’s local package directory. To install in the system wide directory, just move the directory with the package to the system wide package directory OR use the command line version (see below).

Mac:

AddOnManagerDialogMac

 

 

Linux:

 

AddOnManagerDialogLinux

Server machines

For computers without GUI, like high performance clusters, packages can be managed through the command line. An application called ‘packagemanager’ is part of the Linux distribution of BEAST, and has the following options:

 Usage: packagemanager [-list] [-add <NAME>] [-del <NAME>] [-useAppDir] [-dir <DIR>] [-help] 
   -list List available packages
   -add Install the <NAME> package 
   -del Uninstall the <NAME> package 
   -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 package in direcotry <DIR>. This overrides the useAppDir option
   -help Show help

 Examples:
 packagemanager -list
 packagemanager -add SNAPP
 packagemanager -useAppDir -add SNAPP
 packagemanager -del SNAPP

Alternatively the package manager can be launched as

   java -cp beast.jar beast.util.PackageManager

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\<YourName>\BEAST\2.X\VSS
for Mac in /Users/<YourName>\/Library/Application Support/BEAST/2.X/VSS
for Linux /home/<YourName>/.beast/2.X/VSS

Here is the username you use, and in “2.X” the X refers to the major version of BEAST, so 2.X=2.1 for version 2.1.3.

Next, unzip the file VSS.addon.v1.0.0.zip inside the VSS directory

For BEAST v2.5.x and later, you need to reset the class path stored in the beauti.properties file. Easiest to do this is by starting BEAUti and click the menu File/Clear class path. Alternatively, delete the package.path entry from the beauti.properties file. The file is stored in the BEAST package directory (~/.beast/2.5/ for Linux, ~/Library/Application Support/BEAST/2.5/ on OS X, or c:\Users\yourname\BEAST\2.5\ on Windows).

Trouble shooting

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.

Bayesian evolutionary analysis by sampling trees

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