[[Category:Software]]
<languages />
== Description ==

BEAST<ref name="homepage">BEAST2 Homepage: http://beast2.org/</ref> 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<ref>Beagle-lib Homepage: https://github.com/beagle-dev/beagle-lib</ref>, 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: <code>module load beast</code>, will automatically load it's dependencies, namely the <code>beagle-lib</code> and <code>java</code> modules, and set the environment variable <code>EBROOTBEAST</code> 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 <code>packagemanager</code> command (for BEAST v2.5.1 and newer; in older versions of BEAST, the command is <code>addonmanager</code>) to install the desired packages within your home directory.
<tabs>
<tab name="Beast &ge; 2.5.x" >
  $ 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
  [...]
</tab>
<tab name="Beast &le; 2.4.x">
  $ 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
  [...]
</tab>
</tabs>

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
  |name=simple_beast_job.sh
  |lang="sh"
  |contents=
#!/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
  |name=high_memory_beast_job.sh
  |lang="sh"
  |contents=
#!/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 -cp ${BEAST_LIB}/launcher.jar beast.app.beastapp.BeastLauncher" # which program to execute

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

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

}}

== References ==
<references />