BEAST

module avail beast/
module avail beast2/

BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology.

Usage

Parallel run

For parallel running, additional parameters are required

-instances N -threads N

where N is the number of processors requested in the PBS task. And also add

useThreads="true" 

attribute in the input file.

With BEAGLE

# Load BEAST, e.g.
module add beast2/beast2-2.6.7-intel-19.0.4-d2lg5zn
# Load OpenJDK
module add openjdk/openjdk-1.8.0_222-b10-intel-19.0.4-xc66unh
# Load BEAGLE
module add libbeagle/libbeagle-3.1.2-intel-19.0.4-gpu-m62lgl6
# See available graphical cards (if applicable) and help
beast -beagle_info
beast -help
# Use BEAST with BEAGLE
beast ... -beagle ... XXX.xml

Beast additional packages

Users can install additional packages available via the packagemager command in their home directories. The following example demonstrates the local building of Beast 2.7.7 (distributed as a binary file; no installation is required) and the installation of the SNAPP package.

$ wget https://github.com/CompEvol/beast2/releases/download/v2.7.7/BEAST.v2.7.7.Linux.x86.tgz
$ tar -xf BEAST.v2.7.7.Linux.x86.tgz
$ export PATH=/storage/city/home/user_name/beast/bin/:$PATH

The default installation of Beast includes only Beast and Java.

$ beast -version
BEAST v2.7.7
---
BEAST.app v2.7.7
BEAST.base v2.7.7
BEAST.app v2.7.7
BEASTLabs v2.0.2
---
Java version 17.0.3

If the SNAPP package is installed in the same directory as Beast itself, the package will be detected automatically.

$ packagemanager -add SNAPP -dir /storage/city/home/user_name/beast
$ beast -version
BEAST v2.7.7
---
BEAST.app v2.7.7
BEAST.base v2.7.7
BEAST.app v2.7.7
SNAPP v1.6.1
BEASTLabs v2.0.2
---
Java version 17.0.3

But if the package is located in a different (non-automatically detected) path, it is necessary to specify this path via the -packagedir option in the beast command.

$ beast -packagedir /storage/city/home/username/folder_with_packages