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Parallel and MPI Octave

There are some excellent packages for GNU Octave, the free and open-source numerical computation language that is "highly compatible" with the proprietary and closed-source MATLAB (tm).

Some Interesting R Library Quirks

A researcher uses an HPC system to analyse DNA methylation data. However when they try to install some related libraries, the installation fails.

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

General Atomic and Molecular Electronic Structure System HPC Installation

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 (Just Another Gibbs Sampler) Installation

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
tar xvf JAGS-3.4.0.tar.gz
mv JAGS-3.4.0 jags-3.4.0
cd jags-3.4.0
make check
make install
make installcheck

The config script takes the following form

install=$(basename $(pwd) | sed 's%-%/%')

MuTect Installation

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.

PROJ.4 Cartographic Projections library installation

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

Download, extract, install.

cd /usr/local/src/PROJ
tar xvf proj-4.9.1.tar.gz
cd proj-4.9.1
make check
make install

The config file is a quick executable.

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

Geospatial Data Abstraction Library Installation

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

Download, extract, install.

cd /usr/local/src/GDAL
tar gdal-1.11.2.tar.gz
cd gdal-1.11.2
make install

The config file is a quick executable.

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

Rosetta Proteins with SCons (and jam and cream)

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 with Modules

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
tar xvf scons-2.3.4.tar.gz
cd scons-2.3.4
python 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

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