BEAST 2.6.3

Basic information

  • Official Website: http://www.beast2.org/

  • License: GNU LESSER GENERAL PUBLIC LICENSE Version 2.1

  • Installed on: Apolo II

  • Installation date: 23/02/2021

Tested on (Requirements)

  • OS base: CentOS (x86_64) \(\boldsymbol{\ge}\) 6.6 (Rocks 6.2)

  • Dependencies:

    • Java JDK - 1.8.0 u112

Installation

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

    cd /home/blopezp/Desktop/BEAST
wget https://github.com/CompEvol/beast2/releases/download/v2.6.3/BEAST.v2.6.3.Linux.tgz
tar -zxvf BEAST.v2.6.3.Linux.tgz
2. After unpacking blast, continue with the following steps to finish the installation:

  2. After unpacking blast, continue with the following steps to finish the installation:

    cd beast
sudo mkdir -p /share/apps/beast2/2.6.3
sudo cp -r bin/ lib/ templates / examples/ images/ /sahre/apps/beast2/2.6.3
ls -p /share/apps/beast2/2.6.3

Module

#%Module1.0#####################################################################
##
## module beast2/2.6.3
##
## /share/apps/modules/beast2/2.6.3 Written by Bryan López Parra
##

proc ModulesHelp { } {
    puts stderr "\tbeast2/2.6.3 - sets the Environment for BEAST2 \
    \n\tin the share directory /share/apps/beast2/2.6.3\n"
}

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

# for Tcl script use only
set     topdir          /share/apps/beast2/2.6.3
set     version         2.6.3
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 beast2/2.6.3

Slurm template

#!/bin/bash
#SBATCH --job-name=BEAST2-2.6.0-case
#SBATCH --partition=batch
#SBATCH --nodes=1
#SBATCH --ntasks=8
#SBATCH --time=1:00:00

module load beast2/2.6.3

beast -threads $SLURM_NTASKS testStarBeast.xml

Resources

Author: