BEAST

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This site replaces the former Compute Canada documentation site, and is now being managed by the Digital Research Alliance of Canada.

Ce site remplace l'ancien site de documentation de Calcul Canada et est maintenant géré par l'Alliance de recherche numérique du Canada.

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Description

BEAST[1] 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. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability.

BEAST can use the beagle-lib[2], which is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.

Usage

Loading the BEAST module with: module load beast, will automatically load it's dependencies, namely the beagle-lib and java modules, and set the environment variable EBROOTBEAST to point to the directory where BEAST's program files are located.

Managing BEAST Packages/Add-ons

BEAST has been installed without any packages (add-ons). You can use the packagemanager command (for BEAST v2.5.1 and newer; in older versions of BEAST, the command is addonmanager) to install the desired packages within your home directory.

 $ module load beast/2.5.1
 $ packagemanager -list
 Name    | Installation Status | Latest Version | Dependencies | Description
 --------------------------------------------------------------------------
 BEAST   | 2.5.1               | 2.5.0          |              | BEAST core
 --------------------------------------------------------------------------
 bacter  | NA                  | 2.2.0          |              | Bacterial ARG inference.
 BADTRIP | NA                  | 1.0.0          |              | Infer transmission time for [...]
 [...]
 SNAPP   | NA                  | 1.4.1          |              | SNP and AFLP Phylogenies
 [...]
   
 $ packagemanager -add SNAPP
 Package SNAPP is installed in ~/.beast/2.5/SNAPP.
 
 $ packagemanager -list
 Name    | Installation Status | Latest Version | Dependencies | Description
 --------------------------------------------------------------------------
 BEAST   | 2.5.1               | 2.5.0          |              | BEAST core
 --------------------------------------------------------------------------
 [...]
 SNAPP   | 1.4.1               | 1.4.1          |              | SNP and AFLP Phylogenies
 [...]
 $ module load beast/2.4.0
 $ addonmanager -list
 Name    | Installation Status | Latest Version | Dependencies | Description
 ---------------------------------------------------------------------------
 BEAST   | 2.4.0               | 2.4.8          |              | BEAST core
 ---------------------------------------------------------------------------
 bacter  | not installed       | 1.2.3          |              | Bacterial ARG inference.
 BASTA   | not installed       | 2.3.2          |              | Bayesian structured coalescent approximation
 [...]
 SNAPP   | not installed       | 1.3.0          |              | SNP and AFLP Phylogenies
 [...]
 
 $ addonmanager -add SNAPP
 Package SNAPP is installed in ~/.beast/2.4/SNAPP.
 
 $ addonmanager -list
 Name    | Installation Status | Latest Version | Dependencies | Description
 ---------------------------------------------------------------------------
 BEAST   | 2.4.0               | 2.4.8          |              | BEAST core
 ---------------------------------------------------------------------------
 [...]
 SNAPP   | 1.3.0               | 1.3.0          |              | SNP and AFLP Phylogenies
 [...]

For more information on how to manage BEAST packages please read the section "Server machines" at: http://www.beast2.org/managing-packages/

Simple Jobscript for BEAST

File : simple_beast_job.sh

#!/bin/bash
#SBATCH --account=def-someuser
#SBATCH --time=3:00:00
#SBATCH --mem-per-cpu=2000M

module load beast/2.6.3

beast input_beast.xml


Jobscript for BEAST with more Memory

File : high_memory_beast_job.sh

#!/bin/bash
#SBATCH --account=def-someuser
#SBATCH --time=3:00:00
#SBATCH --mem-per-cpu=4000M

# Increase Maximum memory here if necessary:
# "BEAST_MEM" needs to be 250M lower than "--mem="
BEAST_MEM="-Xmx3750M"

module load beast/2.6.3

# Define variables where to find BEAST and BEAGLE-lib
BEAST_LIB="${EBROOTBEAST}/lib"
BEAST_EXTRA_LIBS="${BEAST_LIB}:${BEAGLE_LIB}"
export LD_LIBRARY_PATH="${BEAGLE_LIB}:${LD_LIBRARY_PATH}"

# Build a long java command:
CMD="java -Xms256m ${BEAST_MEM}"                   # set memory
CMD="$CMD -Djava.library.path=${BEAST_EXTRA_LIBS}" # point to libraries
CMD="$CMD -jar ${BEAST_LIB}/beast.jar"             # which program to execute

echo ".................................."
echo "The Java command is \"${CMD}\""
echo ".................................."

# Run the command:
$CMD -beagle  input_beast.xml


References

  1. BEAST2 Homepage: http://beast2.org/
  2. Beagle-lib Homepage: https://github.com/beagle-dev/beagle-lib