BEAST 2.6.4

Basic information

  • Official Website: http://www.beast2.org/
  • License: GNU LESSER GENERAL PUBLIC LICENSE Version 2.1
  • Installed on: Apolo II
  • Installation date: 08/06/2021

Tested on (Requirements)

  • Dependencies:
    • Java JDK - 1.8.0 u112

Installation

  1. Download the desired version of the software (Source code - tar.gz)

    cd /home/jpossaz/sources/beast2
wget -O beast2.6.4.tgz "https://github-releases.githubusercontent.com/15949777/faf69900-ae6f-11eb-8247-ca2b5a96b6dd?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210608%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210608T204641Z&X-Amz-Expires=300&X-Amz-Signature=4edf797e065ec87baa8a21dbd0cd5938f85a56d0f03e25535125646c65cfdbc2&X-Amz-SignedHeaders=host&actor_id=13303029&key_id=0&repo_id=15949777&response-content-disposition=attachment%3B%20filename%3DBEAST.v2.6.4.Linux.tgz&response-content-type=application%2Foctet-stream"
tar -zxvf beast2.6.4.tgz

  2. After unpacking, copy the files to the corresponding apps directory:

    cd beast
sudo mkdir -p /share/apps/beast2/2.6.4
sudo cp -r bin/ lib/ templates/ examples/ images/ /share/apps/beast2/2.6.4

Module

#%Module1.0#####################################################################
##
## module /share/apps/modules/beast2/2.6.4
##
## /share/apps/beast2/2.6.4 Written by Juan Pablo Ossa Zapata
##

proc ModulesHelp { } {
    puts stderr "\tbeast2/2.6.4 - sets the Environment for BEAST2 \
    \n\tin the share directory /share/apps/beast2/2.6.4\n"
}

module-whatis "\n\n\tSets the environment for using beast2\n"

# for Tcl script use only
set     topdir          /share/apps/beast2/2.6.4
set     version         2.6.4
set     sys             linux-x86_64

conflict beast2

module load java/jdk-1.8.0_112

prepend-path PATH               $topdir/bin

prepend-path CLASSPATH          $topdir/lib/beast.jar
prepend-path CLASSPATH          $topdir/lib/beast.src.jar
prepend-path CLASSPATH          $topdir/lib/DensiTree.jar
prepend-path CLASSPATH          $topdir/lib/launcher.jar

Use

module load beast2/2.6.4

Example slurm job file:

#!/bin/sh
#SBATCH --partition=longjobs
#SBATCH --nodes=1
#SBATCH --cpus-per-task=4
#SBATCH --ntasks=1
#SBATCH --time=2:00:00
#SBATCH --job-name=testBEAST2
#SBATCH -o %x_%j.out      # File to which STDOUT will be written
#SBATCH -e %x_%j.err      # File to which STDERR will be written
#SBATCH --mail-type=ALL
#SBATCH --mail-user=jpossaz@eafit.edu.co

module load beast2/2.6.4
export OMP_NUM_THREADS=4
DISPLAY="" beast -threads 4 testRNA.xml

Make sure that your xml file can and will use all of the threads that you assign to the job.

Author

  • Juan Pablo Ossa Zapata