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 packages 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 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).
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:
Alternatively the package manager can be launched as
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
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
Easiest to do this is by starting BEAUti and click the menu
File/Clear class path.
Alternatively, delete the
package.path entry from the
The file is stored in the BEAST package directory (
~/.beast/2.X/ for Linux,
~/Library/Application Support/BEAST/2.X/ on OS X, or
c:\Users\yourname\BEAST\2.X\ on Windows).
Adding package repositories by handBy default, packages will be sourced from https://github.com/CompEvol/CBAN/blob/master/packages2.6.xml for BEAST v2.6.x. You can specify other package sources in BEAUti in the package manager by clicking the package repositories button, and a dialog pops up where you can add entries.
These entries are stored in beauti.properties file in the package directory has an entry for packages.url. Instead of managing these repositories through BEAUti, you can edit the file with a text editor. For example, if you set this entry to
(note the \ before :) the package manager will pick up packages from https://raw.githubusercontent.com/CompEvol/CBAN/master/packages-extra.xml.
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.