Research Infrastructure

Beast

Background

http://www.beast2.org/

August 2022 – Upasana Singh requested beast2 to be installed (isr:573293).

BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies 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 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. BEAST 2 includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results.

BEAST 2 is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version

Installation Steps 2.6.7

APPROOT=/opt/apps/apps/binapps/beast2
APPVER=2.6.7
APPDIR=$APPROOT/${APPVER}

cd $APPROOT
sudo mkdir -p $APPDIR
sudo chown -R ${USER}. $APPDIR

mkdir -p archive
cd archive
module load tools/env/proxy2
wget --no-check-certificate https://github.com/CompEvol/beast2/releases/download/v2.6.7/BEAST.v2.6.7.Linux.tgz

cd ${APPDIR}/${APPVER}
tar -xzvf ../archive/BEAST.v${APPVER}*


Module File

/opt/apps/modules/apps/binapps/beast2

#%Module1.0####################################################
##
## beast2 Modulefile
##
##
proc getenv {key {defaultvalue {}}} {
  global env; expr {[info exist env($key)]?$env($key):$defaultvalue}
}

proc ModulesHelp { } {
	global APPVER APPNAME APPCSFURL APPURL 

	puts stderr "
	Adds $APPNAME $APPVER to your PATH environment variable and any necessary
	dependent modulefiles.

	For information on how to run $APPNAME on the CSF please see:
	$APPCSFURL
	
	For application specific info see:
	$APPURL
"
}

set	APPVER		2.6.7
set	APPNAME		beast2
set	APPNAMECAPS	BEAST2
set	APPCSFURL	https://ri.itservices.manchester.ac.uk/csf3/software/applications/$APPNAME
set	APPURL		https://www.beast2.org
set     COMPDIR         binapps

module-whatis    "Adds $APPNAME $APPVER to your environment"
module load tools/java/1.8.0

set	APPROOT			/opt/apps/apps/$COMPDIR/$APPNAME
set     APPDIR   		/opt/apps/apps/$COMPDIR/$APPNAME/$APPVER

setenv	${APPNAMECAPS}ROOT	$APPROOT
setenv  ${APPNAMECAPS}DIR	$APPDIR
setenv  ${APPNAMECAPS}_HOME	$APPDIR

# Typical env vars needed to run an app

prepend-path    PATH                    $APPDIR/beast/bin/
#prepend-path   LD_LIBRARY_PATH         $APPDIR/lib64
#prepend-path	MANPATH			$APPDIR/share/man

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