Installing BEAST on a 64-bit AMD Opteron Cluster running CentOS 5 Linux

BEAST (Bayesian Evolutionary Analysis Sampling Trees ) "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".

To install BEAST download the tarball from the website, extract, change into the native directory, load the environment variables for Java >1.5, run a make and cp the shared object dynamic library files to the library directory. Copy the results to /usr/local/BEAST and create an environment module.


cd /usr/local/src/BEAST
wget http://beast-mcmc.googlecode.com/files/BEASTv1.6.1.tgz
tar zxf BEASTv1.6.1.tgz
mv BEASTv1.6.1 1.6.1
cd 1.6.1/native
module load java/1.6.0_13
make -f Makefile.icc
cp libNucleotideLikelihoodCore.so ../lib
cd /usr/local/Modules/modulefiles/beast
ln -s .base 1.6.1

The .base module file looks like the following:


#%Module1.0#####################################################################
##
## $name modulefile
##
set ver [lrange [split [ module-info name ] / ] 1 1 ]
set name [lrange [split [ module-info name ] / ] 0 0 ]
set loading [module-info mode load]
proc ModulesHelp { } {
puts stderr "\tThis module sets the envinronment for $name v$ver"
}
module-whatis "Set environment variables to use $name version $ver"
if { $loading && ![ is-loaded java ] } {
module load java
}
prepend-path LD_LIBRARY_PATH /usr/local/$name/$ver/lib
prepend-path PATH /usr/local/$name/$ver/bin
prepend-path PATH /usr/local/$name/$ver