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MrBayes HPC Installation

Mr. Bayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.

Download, extract. Note that the developers have produced a tarbomb which will require a separate directory created before download. This has been raised as a bug.

Note that more recent versions of MrBayes make much better use of autoconfiguration tools.


cd /usr/local/src/MRBAYES
mkdir mrbayes-3.2.5
cd mrbayes-3.2.5
wget http://downloads.sourceforge.net/project/mrbayes/mrbayes/3.2.5/mrbayes-3...
tar xvf mrbayes-3.2.5.tar.gz


module load openmpi-gcc/1.8.4
module load beagle/20150401
mkdir -p /usr/local/mrbayes/3.2.5
./configure --enable-mpi=yes --with-beagle=/usr/local/beagle/20150401
make
cp mb /usr/local/mrbayes/3.2.5/

Create link to the module files.


cd /usr/local/Modules/modulefiles/mrbayes
ln -s .base 3.2.5

The .base file has the following form:


#%Module1.0#####################################################################
##
## $name modulefile
##
set ver [lrange [split [ module-info name ] / ] 1 1 ]
set name [lrange [split [ module-info name ] / ] 0 0 ]
set loading [module-info mode load]
set desc [join [read [ open "/usr/local/Modules/modulefiles/$name/.desc" ] ] ]
proc ModulesHelp { } {
puts stderr "This module sets the envinronment for $name v$ver"
}
module-whatis "$desc (v$ver)"
prepend-path PATH /usr/local/$name/$ver

Note that this is a substantial revision of previous installations.