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

GAMESS (General Atomic and Molecular Electronic Structure System (GAMESS)) is a general ab initio quantum chemistry package. You will need to agree to the license prior to download, which will provide a link to gamess-current.tar.gz

Download and extract, load the environment variables for atlas and gcc.


cd /usr/local/src/
tar gamess-current.tar.gz
cd gamess
module load atlas/3.10.2
module load gcc/4.9.1


JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS.


cd /usr/local/src/JAGS
wget http://downloads.sourceforge.net/project/mcmc-jags/JAGS/3.x/Source/JAGS-3.4.0.tar.gz
tar xvf JAGS-3.4.0.tar.gz
mv JAGS-3.4.0 jags-3.4.0
cd jags-3.4.0
../config
make
make check
make install
make installcheck


The config script takes the following form


#!/bin/bash
install=$(basename $(pwd) | sed 's%-%/%')

MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.

For complete details, please see the publication in Nature Biotechnology:

Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnology (2013).doi:10.1038/nbt.2514

Download after login.

The PROJ.4 Cartographic Projections library was originally written by Gerald Evenden then of the USGS.

Download, extract, install.


cd /usr/local/src/PROJ
wget http://download.osgeo.org/proj/proj-4.9.1.tar.gz
tar xvf proj-4.9.1.tar.gz
cd proj-4.9.1
../config
make
make check
make install


The config file is a quick executable.


#!/bin/bash
./configure --prefix=/usr/local/$(basename $(pwd) | sed 's#-#/#')


GDAL (Geospatial Data Abstraction Library) is a translator library for raster and vector geospatial data formats.

Download, extract, install.


cd /usr/local/src/GDAL
wget http://download.osgeo.org/gdal/1.11.2/gdal-1.11.2.tar.gz
tar gdal-1.11.2.tar.gz
cd gdal-1.11.2
../config
make
make install


The config file is a quick executable.


#!/bin/bash
./configure --prefix=/usr/local/$(basename $(pwd) | sed 's#-#/#')


Rosetta is a library based object-oriented software suite which provides a robust system for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions.

You'll need a license

Download, extract, load scons, and compile.


cd /usr/local/src/ROSETTA
tar xvf rosetta_src_2015.19.57819_bundle.tgz
cd rosetta_src_2015.19.57819_bundle/main/src
module load scons
scons


SCons is a software construction tool (build tool, or make tool) implemented in Python, that uses Python scripts as "configuration files" for software builds.


cd /usr/local/src/SCONS
wget http://prdownloads.sourceforge.net/scons/scons-2.3.4.tar.gz
tar xvf scons-2.3.4.tar.gz
cd scons-2.3.4
python setup.py install --prefix=/usr/local/scons/2.3.4


Change to the appropriate modules directory, check for .desc and .version and .base, create a symblink to .base


cd /usr/local/Modules/modulefiles/scons
ln -s .base 2.3.4

Freesurfer is a set of tools for analysis and visualization of structural and functional brain imaging data.

Check system requirements and download. Note that registration and a license key is required for functionality, but not installation.

Create a source directory, change to it, download, extract, discover that everything is bundled, create the application directory and move everything across.

The use of cloud computing as an alternative implementation for high performance computing (HPC) initially seems to be appealing, especially to IT managers and to users who may find the jump from their desktop application to the command line interface challenging. However a careful and nuanced review of metrics should lead to a reconsideration of these assumptions.