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== Installed software ==
This page shows a list of installed modules on the [[Cheaha]] research computing system. If you don't find a particular package listed on this page, please send a request to [mailto:support@vo.uabgrid.uab.edu cheaha support] to request the software.


We try to install local software in /opt, /opt/uabeng and /share/apps. However, please do not depend on a particular piece of software being in a specific directory, as we may need to move things around at some point.
This list is not exhaustive and may not reflect the accurate current versions of the different software installed on the system. Please see the output of the '''module avail''' command for the official list of software modules installed on Cheaha.


In most cases, the descriptions for each software package was copied from the authors web site and represents their own work.
==Software modules installed on Cheaha==
 
{| border="1" align="center" cellpadding="10" style="text-align:center;"
If you don't find a particular package listed on this page, please send a request to [mailto:support@vo.uabgrid.uab.edu cheaha support] to request the software.
|+
 
! Software
If a module file is available for the software, it is recommended to use the module file in your job script and/or shell profile.
! Latest Version
 
! Other Versions
{| border="1" cellpadding="2"
! Remarks
!Software (Link to home page)
|-
!Version
|'''[[AFNI]]'''
!Software Installation-Directory
|AFNI_Jun_25_2013
!Information
|AFNI_2011_12_21_1014
|linux openmp 64, linux Xorg7 64
|-
|'''[[Affymetrix]]'''
|1.14.3
|
|
|-
|-
|[http://ambermd.org/ Amber]
|'''[[Amber]]'''
|10
|10
|/opt/uabeng/amber10/intel
|
|"Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.
|
 
|-
Amber is compiled using Intel compilers and uses OpenMPI for the parallel binaries.
|'''[[ANNOVAR]]'''
 
|2012Feb23
The following Modules files should be loaded for this package (the amber module will automatically load the openmpi module):
|
 
|ngs-ccts 2013.09.11/2013.04.03
For Intel:
|-
<pre>
|'''[[ANSYS]]'''
module load amber/amber-10-intel
|14.5
</pre>
|14.0
 
|
Use the '''openmpi''' parallel environment in your job script (example for a 4 slot job)
|-
<pre>
|'''[[APBS]]'''
#$ -pe openmpi 4
|1.0
</pre>
|
|
|-
|-
|[http://apbs.sourceforge.net/ APBS]
|'''[[Aspera]]'''
|1.0.0
|2.4.7
|/share/apps/apbs/apbs-1.0.0-amd64
|
|APBS - Adaptive Poisson-Boltzmann Solver ''APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media.''
|
 
Submit APBS jobs via the Grid Engine and do not run them on the head node!
 
<pre>
module load apbs/apbs-1.0
</pre>
 
|-
|-
|[http://math-atlas.sourceforge.net/ Atlas]
|'''[[Atlas]]'''
|3.8.3
|3.8
|/usr/lib64/atlas
|
|The ATLAS (Automatically Tuned Linear Algebra Software) project is an
|
ongoing research effort focusing on applying empirical techniques in
order to provide portable performance. At present, it provides C and
Fortran77 interfaces to a portably efficient BLAS implementation, as
well as a few routines from LAPACK.
 
<pre>
module load atlas/atlas
</pre>
|-
|-
|[http://biopython.org/wiki/Main_Page Biopython]
|'''[[AutoDock]]'''
|1.51
|4.2.3
|
|
|
|Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. 
The Biopython packages along with its dependencies (Numpy, python-reportlab, Flex, etc...) are all installed in the default location for Python site-packages, so you should not need to modify any environment variables to use this package.
|-
|-
|[http://www.broad.mit.edu/science/programs/medical-and-population-genetics/birdsuite/birdsuite-0 Birdsuite]
|'''[[Birdsuite]]'''
|1.5.5
|1.5.3
|1.5.3
|/share/apps/birdsuite/1.5.3
|
|The Birdsuite is a fully open-source set of tools to detect and report SNP genotypes, common Copy-Number Polymorphisms (CNPs), and novel, rare, or de novo CNVs in samples processed with the Affymetrix platform. While most of the components of the suite can be run individually (for instance, to only do SNP genotyping), the Birdsuite is especially intended for integrated analysis of SNPs and CNVs. Support for chips and platforms other than the Affymetrix SNP 6.0 is currently limited, but we are currently working on creating the supporting files for other common genotyping platforms.  
|-
 
|'''[[Bowtie]]'''
An example job submission script can be found here (copy this to your job directory and make sure to edit the email address!)
|0.9
<pre>
|0.10,0.12
/share/apps/example-scripts/birdsuite-job.qsub
|ngs-ccts 2.1.0
</pre>
|-
 
|'''[[bwa]]'''
The following Modules files should be loaded for this package:
|0.6.2
<pre>
|0.5.10,0.5.9
module load birdsuite/birdsuite-1.5
|ngs-ccts
</pre>
|-
|'''[[cgatools]]'''
|1.8.0
|1.7.1,1.5.0
|ngs-ccts
|-
|'''[[CHASE]]'''
|1
|
|
|-
|'''[[cmake]]'''
|2.8.10.2
|
|
|-
|'''[[CUDA]]'''
|4
|
|
|-
|'''[[COMSOL]]'''
|4.2
|
|
|-
|'''[[Cufflinks]]'''
|0.9
|
|ngs-ccts 2.1.1
|-
|'''[[DSSP]]'''
|2.0.4
|
|
|-
|'''[[Eclipse]]'''
|4.3.1
|
|
|-
|-
|[http://www.boost.org boost]
|'''[[eigenstrat]]'''
|1.33.1
|2.0
|/usr/lib
|
 
|
/usr/lib64
|Boost provides free peer-reviewed portable C++ source libraries.
 
The Boost team emphasize libraries that work well with the C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications. The Boost license encourages both commercial and non-commercial use.
 
Both 32bit and 64bit versions of Boost C++ libraries are provided under /usr/lib and /usr/lib64
|-
|-
|[http://bowtie-bio.sourceforge.net/index.shtml Bowtie]
|'''[[EMAN2]]'''
|0.10.1
|2.02
|/share/apps/bowtie/bowtie-0.10.1
|
|Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end). It supports alignment policies equivalent to Maq  and SOAP but is substantially faster.
|??
 
A Bowtie tutorial is available here: http://bowtie-bio.sourceforge.net/tutorial.shtml
 
The following Modules files should be loaded for this package:
<pre>
module load bowtie/bowtie-0.10
</pre>
|-
|-
|[http://genepath.med.harvard.edu/~reich/Software.htm eigenstrat]
|'''[[ENT]]'''
|3.0
|1.0.2
|/share/apps/eigenstrat
|
|EIGENSTRAT also provides a decent FAQ on their website, [http://www.hsph.harvard.edu/faculty/alkes-price/files/eigensoftfaq.htm click here].
|
 
"The EIGENSOFT package combines functionality from our population genetics methods ([http://www.plosgenetics.org/article/info%3Adoi/10.1371/journal.pgen.0020190 Patterson et al. 2006]) and our EIGENSTRAT stratification method ([http://www.nature.com/ng/journal/v38/n8/abs/ng1847.html Price et al. 2006]). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker's variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes."
 
The following Modules file should be loaded for this package:
<pre>
module load eigenstrat/eigenstrat
</pre>
 
|-
|-
|[http://depts.washington.edu/ventures/UW_Technology/Express_Licenses/fastPHASE.php fastPHASE]
|'''[[fastPHASE]]'''
|1.4.0
|1.4
|/share/apps/fastPHASE/1.4
|
|The program fastPHASE implements methods for estimating haplotypes and missing genotypes from population SNP genotype data.
|
 
The following Modules files should be loaded for this package:
 
<pre>
module load fastphase/fastphase-1.4
</pre>
 
|-
|-
|[http://www.fftw.org/ FFTW]
|'''[[FFTW]]'''
|3.1.2
|3.1.2
|/opt/uabeng/fftw3/gnu
|
 
|gnu/intel
/opt/uabeng/fftw3/intel
|-
 
|'''[[FreeSurfer]]'''
|FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).  
|5.3.0
 
|4.5,5.2.0
The following Modules files should be loaded for this package:
|
 
|-
For GNU:
|'''[[FREGENE]]'''
<pre>
|2008
module load fftw/fftw3-gnu
|
</pre>
|
For Intel:
|-
<pre>
|'''[[Fsl]]'''
module load fftw/fftw3-intel
|5.0.6
</pre>
|4.1.6
 
|
|-
|'''[[Galaxy]]'''
|1.0
|
|
|-
|'''[[gcc]]'''
|4.8.1
|
|
|-
|'''[[genn]]'''
|
|
|
|-
|-
|[http://www.gromacs.org/ Gromacs]
|'''[[Gromacs]]'''
|4.0.5
|4.6.1
|/opt/uabeng/gromacs/gnu/4
|4,4.5
 
|gnu/intel
/opt/uabeng/gromacs/intel/4
|GROMACS is a versatile package to perform molecular dynamics and is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
 
Gromacs is compiled using Intel and GNU compilers using FFTW3, BLAS, and LAPACK and OpenMPI for the parallel binaries. Single and double precision binaries are included (double precision binaries have a _d suffix).
 
The following Modules files should be loaded for this package (module will automatically load any prerequisite modules):
 
For GNU:
<pre>
module load gromacs/gromacs-4-gnu
</pre>
For Intel:
<pre>
module load gromacs/gromacs-4-intel
</pre>
 
Use the '''openmpi''' parallel environment in your job script (example for a 4 slot job)
<pre>
#$ -pe openmpi 4
</pre>
|-
|-
|[http://www.gnu.org/software/gsl/ GSL]
|'''[[GTOOL]]'''
|1.10
|0.6.7
|/usr/lib
|
 
|
/usr/lib64
 
/usr/include/gsl
 
|The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License.
 
The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.
|-
|-
|[http://www.stats.ox.ac.uk/~marchini/software/gwas/hapgen.html HAPGEN]
|'''[[HAPGEN]]'''
|1.3.0
|1.3.0
|/share/apps/hapgen/1.3.0
|
|HAPGEN is a program thats simulates case control datasets at SNP markers and can output data in the FILE FORMAT used by IMPUTE, SNPTEST  and GTOOL. The approach can handle markers in LD and can simulate datasets over large regions such as whole chromosomes. Hapgen simulates haplotypes by conditioning on a set of population haplotypes and an estimate of the fine-scale recombination rate across the region.
|
 
|-
Command line syntax example for HAPGEN can be found by [http://www.stats.ox.ac.uk/~marchini/software/gwas/hapgen.html#Running_HAPGEN_top clicking here].
|'''[[Haskell/GHC]]'''
|6.10.4
The HAPGEN environment module can be loaded as follows
|
<pre>
|
module load hapgen/hapgen
|-
</pre>
|'''[[HYPERWORKS]]'''
 
|12.0
|
|
|-
|-
|[https://mathgen.stats.ox.ac.uk/impute/impute_v2.html IMPUTE v2]
|'''[[Illuminus]]'''
|2.0.3
|2
|/share/apps/impute/2.0.3
|
|IMPUTE v2 is a new genotype imputation algorithm based on ideas described in [https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#reference_2 Howie et al. (2009)].
|
 
For the specific version
<pre>
module load impute/impute-2.0.3
</pre>
 
Or to use the latest
<pre>
module load impute/impute
</pre>
 
Examples for IMPUTE v2 are provided in the '''$IMPUTEHOME/Example''' directory.
 
|-
|-
|[http://www-fis.iarc.fr/~martyn/software/jags/ JAGS]
|'''[[IMPUTE2]]'''
|1.0.3
|2.3.0
|/share/apps/jags/jags-1.0.3/gnu
|2.1.2,2.1.0, 2.0.3
|JAGS (Just Another Gibbs Sampler) is a Bayesian hierarchical model analysis program using Markov Chain Monte Carlo (MCMC) simulation. It is similar to [http://mathstat.helsinki.fi/openbugs BUGS] but will compile on Linux systems.
|
 
Click [http://streaming.stat.iastate.edu/wiki/index.php/JAGS_Guide here] for a good description of JAGS and how it differs from BUGS.
 
The JAGS environment module can be loaded as follows
<pre>
module load jags/jags-1.0-gnu
</pre>
 
 
|-
|-
|[http://java.sun.com/javase/technologies/ Java JDK]
|'''[[JAGS]]'''
|1.5.0_10
|1.0
|/usr/java/jdk1.5.0_10
|
|JDK (Java Developers Kit) and Runtime from Sun
|gnu
|-
|-
|[http://java.sun.com/javase/technologies/ JRE]
|'''[[LAM-MPI]]'''
|1.6.0_04
|7.1
|/usr/java/jre1.6.0_04
|
|Java Runtime
|gnu/intel
|-
|-
|[http://www.intel.com/cd/software/products/asmo-na/eng/compilers/284132.htm Intel]
|'''[[LS-DYNA]]'''
|10.1.015
|9.7.1
|/opt/intel/cce
|
 
|
/opt/intel/fce
 
/opt/intel/mkl
|Intel C, C++ and Fortran compilers along with the Intel Math Kernel Libraries
 
The following Modules file should be loaded for this package:
<pre>
module load intel/intel-compilers-10.1
</pre>
 
|-
|-
|[http://www.lam-mpi.org/ LAM-MPI]
|'''[[MACH]]'''
|7.1.4
|1.0.16
|/opt/uabeng/lam/gnu
|
 
|
/opt/uabeng/lam/intel
|LAM/MPI is now in a maintenance mode. Bug fixes and critical patches are still being applied, but little real "new" work is happening in LAM/MPI. This is a direct result of the LAM/MPI Team spending the vast majority of their time working on our next-generation MPI implementation -- Open MPI.
 
Although LAM is not going to go away any time soon (we certainly would not abondon our user base!) -- the web pages, user lists, and all the other resources will continue to be available indefinitely -- we would encourage all users to try migrating to Open MPI. Since it's an MPI implementation, you should be able to simply recompile and re-link your applications to Open MPI -- they should "just work." Open MPI contains many features and performance enhancements that are not available in LAM/MPI.
 
 
The following Modules files should be loaded for this package (for LAM, you must load this module in your profile script and your job script):
 
For GNU:
<pre>
module load lammpi/lam-7.1-gnu
</pre>
For Intel:
<pre>
module load lammpi/lam-7.1-intel
</pre>
 
In order to use LAM-MPI you must load the module in your ~/.bashrc script along with your job submit script. Add the following to your ~/.bashrc (replace -intel with -gnu if using GNU):
 
For Bash Users edit ~/.bashrc:
<pre>
module load lammpi/lam-7.1-intel
</pre>
For Csh Users edit ~/.cshrc:
<pre>
module load lammpi/lam-7.1-intel
</pre>
 
Use the '''lam_loose_rsh''' parallel environment in your job script (example for a 4 slot job)
<pre>
#$ -pe lam_loose_rsh 4
</pre>
|-
|-
|[http://liulab.dfci.harvard.edu/MACS/ MACS]
|'''[[MACS]]'''
|1.3.6
|1.3.6
|/share/apps/macs/1.3.6
|
|Next generation parallel sequencing technologies made chromatin immunoprecipitation followed by sequencing (ChIP-Seq) a popular strategy to study genome-wide protein-DNA interactions, while creating challenges for analysis algorithms. We present Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina / Solexa). MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, is publicly available open source, and can be used for ChIP-Seq with or without control samples.
|
 
|-
To load MACS into your environment, use the following module command:
|'''[[Magma]]'''
<pre>
|5.2
module load macs/macs
|
</pre>
|
|-
|-
|[http://maq.sourceforge.net/maq-man.shtml Maq]
|'''[[Maq]]'''
|0.7.1
|0.7.1
|/share/apps/maq/0.7.1
|
|Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines. It is particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has preliminary functions to handle ABI SOLiD data.  
|
 
|-
See the Maq documentation page for usage: http://maq.sourceforge.net/maq-man.shtml
|'''[[MarthLab]]'''
 
|mosaik 0.9.891
The following Modules files should be loaded for this package:
|gigabayes, pyrobayes
<pre>
|
module load maq/maq-0.7
|-
</pre>
|'''[[MATLAB]]'''
|R2013a
|R2009(a,b),R2010(a,b),R2011(a,b),R2012a
|DCS-128
|-
|'''[[MPICH]]'''
|2
|1.2
|gnu/intel
|-
|'''[[mplayer]]'''
|1.1.1
|
|
|-
|'''[[MrBayes]]'''
|3.1.2
|
|intel
|-
|'''[[MVAPICH]]'''
|2
|
|gnu
|-
|'''[[Namd]]'''
|2.9
|2.8,2.7,2.6
|ibverbs
|-
|'''[[OpenMPI]]'''
|1.6.4
|1.2
|gnu/intel
|-
|'''[[ParaView]]'''
|3.12
|3.4,3.6,3.8
|
|-
|'''[[PDT]]'''
|3.19
|3.14,3.17
|
|-
|'''[[PennCNV]]'''
|2010May01
|
|
|-
|'''[[petsc]]'''
|3.4.3
|
|
|-
|'''[[PHASE]]'''
|2.1.1
|
|
|-
|-
|[http://www-unix.mcs.anl.gov/mpi/mpich1/ MPICH]
|'''[[PLINK]]'''
|1.2.7p1
|1.07
|/opt/mpich/gnu
|1.06,1.05
/opt/mpich/intel
|
|GNU and Intel compiled versions of MPICH are installed under this directory
 
The following Modules file should be loaded to use mpich
* GNU version of mpich
<pre>
module load mpich/mpich-1.2-gnu
</pre>
* Intel version of mpich
<pre>
module load mpich/mpich-1.2-intel
</pre>
 
Use the '''mpich''' parallel environment in your job script (example for a 4 slot job)
<pre>
#$ -pe mpich 4
</pre>
|-
|-
|[http://www.ks.uiuc.edu/Research/namd/ NAMD]
|'''[[Python]]'''
|2.7
|2.6
|2.6
|/share/apps/namd/2.6
|
|NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet.  
|-
 
|'''[[R]]'''
The following Modules files should be loaded for this package:
|3.0.1
<pre>
|2.6.2,2.7.2,2.8.1,2.9.0,2.9.2,2.11.1,2.12.2,2.14.2,2.15.0,2.15.3,3.0.0
module load namd/namd-2.6
|
</pre>
|-
 
|'''[[RAxML]]'''
|7.2.6
|
|
|-
|'''[[RNA pipeline]]'''
|0.5.0
|0.31
|
|-
|-
|[http://www.open-mpi.org/ OpenMPI]
|'''[[S.A.G.E.]]'''
|1.3.3
|6.2
|/opt/uabeng/openmpi/gnu
|6.0
 
|
/opt/uabeng/openmpi/intel
|The Open MPI Project is an open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry partners.
 
The following Modules files should be loaded for this package:
 
For GNU:
<pre>
module load openmpi/openmpi-gnu
</pre>
For Intel:
<pre>
module load openmpi/openmpi-intel
</pre>
 
Use the '''openmpi''' parallel environment in your job script (example for a 4 slot job)
<pre>
#$ -pe openmpi 4
</pre>
 
To enable verbose Grid Engine logging for OpenMPI, add the following the mpirun command in the job script '''--mca pls_gridengine_verbose 1''', for example:
<pre>
#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#
#$ -N j_openmpi_hello
#$ -pe openmpi 4
#$ -l h_rt=00:20:00,s_rt=0:18:00
#$ -j y
#
#$ -M USERID@uab.edu
#$ -m eas
#
# Load the appropriate module files
. /etc/profile.d/modules.sh
module load openmpi/openmpi-gnu
 
#$ -V
 
mpirun --mca pls_gridengine_verbose 1 -np $NSLOTS hello_world_gnu_openmpi
 
</pre>
 
|-
|-
|[http://www.stat.washington.edu/stephens/phase/download.html PHASE]
|'''[[SAMtools]]'''
|2.1.1
|0.1
|/share/apps/PHASE/2.1.1
|
|PHASE is software for haplotype reconstruction, and recombination rate estimation from population data. The software implements methods for estimating haplotypes from population genotype data described in:
|ngs-ccts 0.1.19
 
* Stephens, M., and Donnelly, P. (2003).  A comparison of Bayesian methods for haplotype reconstruction from population genotype data. American Journal of Human Genetics, [http://stephenslab.uchicago.edu/MSpapers/Stephens2003a.pdf 73:1162-1169].
* Stephens, M., Smith, N., and Donnelly, P. (2001). A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics, [http://stephenslab.uchicago.edu/MSpapers/Stephens2001.pdf 68, 978--989].
* Stephens, M., and Scheet, P. (2005). Accounting for Decay of Linkage Disequilibrium in Haplotype Inference and Missing-Data Imputation. American Journal of Human Genetics, [http://stephenslab.uchicago.edu/MSpapers/Stephens2005.pdf 76:449-462].
 
 
The software also incorporates methods for estimating recombination rates, and identifying recombination hotspots:
* Crawford et al (2004). Evidence for substantial fine-scale variation in recombination rates across the human genome. [http://stephenslab.uchicago.edu/MSpapers/Crawford2004.pdf Nature Genetics]
 
 
Documentation on the usage of PHASE can be downloaded [http://stephenslab.uchicago.edu/instruct2.1.pdf here].
 
The following Modules files should be loaded for this package:
<pre>
module load phase/phase
</pre>
 
|-
|-
|[http://pngu.mgh.harvard.edu/~purcell/plink/ PLINK]
|'''[[ScaleMP]]'''
|1.06
|3.2.2
|/share/apps/plink/1.06
|
|PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analysis in a computationally efficient manner.
|fftw optimized
 
The PLINK web site also has a [http://pngu.mgh.harvard.edu/~purcell/plink/tutorial.shtml tutorial section] that users should read through.
 
Please see this [http://pngu.mgh.harvard.edu/~purcell/plink/contact.shtml#cite page for PLINK citing instructions].
 
To load PLINK into your environment, use the following module command:
<pre>
module load plink/plink
</pre>
 
The following commands are available
* [http://pngu.mgh.harvard.edu/~purcell/plink/reference.shtml plink] - The plink executable is the primary binary for this software. Click [http://pngu.mgh.harvard.edu/~purcell/plink/reference.shtml here] for the command line reference.
* [http://pngu.mgh.harvard.edu/~purcell/plink/gplink.shtml gplink] - This is a java based GUI for PLINK that provides the following functionality:
**  is a GUI that allows construction of many common PLINK operations
** provides a simple project management tool and analysis log
** allows for data and computation to be on a separate server (via SSH)
** facilitates integration with Haploview 
 
'''Running gplink''': You should NOT run gplink from the cheaha login node (head node), only from the compute nodes using the qrsh command. The qrsh command will provide a shell on a compute node complete with X forwarding. For example:
<pre>
[jsmith@cheaha ~]$ qrsh
 
Rocks Compute Node
Rocks 5.1 (V.I)
Profile built 13:06 21-Nov-2008
 
Kickstarted 13:13 21-Nov-2008
 
[jsmith@compute-0-10 ~]$ module load plink/plink
 
[jsmith@compute-0-10 ~]$ gplink
 
</pre>
 
You should see the gPLINK window open. If you get an error similar to "No X11 DISPLAY variable was set", make sure your initial connection to Cheaha had X forwarding enabled.
 
If you want to use the PLINK R plugin functionality, please see this page http://pngu.mgh.harvard.edu/~purcell/plink/rfunc.shtml for instructions. You'll need to install the Rserve package to use the plugin, for example:
<pre>
install.packages("Rserve")
</pre>
|-
|-
|[http://www.csm.ornl.gov/pvm/pvm_home.html pvm]
|'''[[SHRiMP]]'''
|3.4.5
|1.3
|/usr/bin/pvm
|1.2
|PVM3 (Parallel Virtual Machine) is a library and daemon that allows
|
distributed processing environments to be constructed on heterogeneous
machines and architectures.
 
|-
|-
|[http://www.r-project.org/ R]
|'''[[SOLAR]]'''
|2.7.2
|4.3.1
2.8.1
|
2.9.0
|
2.9.2
2.11.1
|/share/apps/R/2.7.2/gnu
/share/apps/R/2.8.1/gnu
/share/apps/R/2.9.0/gnu
/share/apps/R/2.9.2/gnu
/share/apps/R/2.11.1/gnu
|R is a free software environment for statistical computing and graphics. Please refer to the following page for additional instructions for running R on Cheaha [[R-userinfo|Running R Jobs on a Rocks Cluster]].
 
The following Modules files should be loaded for this package:
<pre>
module load R/R-2.7.2
</pre>
 
For other versions, simply replace the version number
<pre>
module load R/R-2.11.1
</pre>
 
The following libraries are available, additional libraries should be installed by the user under ~/R_exlibs
 
* /share/apps/R/R-<font color="red">X.X.X</font>/gnu/lib/R/library
** The default libraries that come with R
** Rmpi
** Snow
* /share/apps/R/R-<font color="red">X.X.X</font>/gnu/lib/R/bioc
** BioConductor libraries (default package set using getBioC)
 
'''Sample R Grid Engine Job Script'''
This is an example of a serial (i.e. non parallel) R job that has a 2 hour run time limit requesting 256M of RAM
<pre>
#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#
#$ -j y
#$ -N rtestjob
# Use '#$ -m n' instead to disable all email for this job
#$ -m eas
#$ -M YOUR_EMAIL_ADDRESS
#$ -l h_rt=2:00:00,s_rt=1:55:00
#$ -l vf=256M
. /etc/profile.d/modules.sh
module load R/R-2.7.2
 
#$ -v PATH,R_HOME,R_LIBS,LD_LIBRARY_PATH,CWD
 
R CMD BATCH rscript.R
</pre>
 
|-
|-
|[http://darwin.cwru.edu/sage/ s.a.g.e.]
|'''[[SPPARKS]]'''
|6.0.0
|30May11
|/share/apps/s.a.g.e./SAGE_6.0.0_Linux64
|07Aug09
|S.A.G.E. - Statistical Analysis for Genetic Epidemiology contains programs for use in the genetic analysis of family, pedigree and individual data.
|
 
'''Note: This software is NOT the same as the SAGE listed below!'''
<pre>
Make sure that every publication which presents results from using
S.A.G.E. carries an appropriate acknowledgement such as:
 
'(Some of) The results of this paper were obtained by using the program
package S.A.G.E., which is supported by a U.S. Public Health Service
Resource Grant (1 P41 RR03655) from the National Center for Research
Resources'  - (it is important that the grant numbers appear under
'acknowledgments').
 
Send bibliographic information about every paper in which S.A.G.E. is
used (author(s), title, journal, volume and page numbers; a reprint will
do provided it has the necessary information on it) to:
 
R.C. Elston
Department of Epidemiology and Biostatistics
Case Western Reserve University
Wolstein Research Building
2103 Cornell Road
Cleveland, Ohio  44106-7281
 
The recommended way of referencing the S.A.G.E. programs is as follows:
 
S.A.G.E. [2009]. Statistical Analysis for Genetic Epidemiology 6.0
Computer program package available from the Department of Epidemiology and
Biostatistics, Case Western Reserve University, Cleveland.
</pre>
 
Demo data files are available under
/share/apps/s.a.g.e./SAGE_6.0.0_Linux64/demo/data_files
 
To load the S.A.G.E. environment, use
<pre>
module load s.a.g.e./sage-6.0
</pre>
|-
|-
|[http://compbio.cs.toronto.edu/shrimp/ SHRiMP]
|'''[[Structure]]'''
|1.3.2
|2.2
|/share/apps/shrimp/SHRiMP_1_3_2
|
|SHRiMP is a software package for aligning genomic reads against a target genome. It was primarily developed with the multitudinous short reads of next generation sequencing machines in mind, as well as Applied Biosystem's colourspace genomic representation.
|
 
The following Modules files should be loaded for this package:
<pre>
module load shrimp/shrimp-1.3
</pre>
|-
|-
|[http://sprng.fsu.edu/ SPRNG]
|'''[[tabix]]'''
|2.0a
|0.2.6
|/share/apps/sprng/2.0a
|
|Scalable Parallel Pseudo Random Number Generators Library
|ngs-ccts
 
The following Modules files should be loaded for this package:
<pre>
module load sprng/sprng-2
</pre>
|-
|-
|[http://subversion.tigris.org/ Subversion]
|'''[[TAU]]'''
|1.4.2
|2.22.2
|/usr/bin/svn
|2.21.1
|Subversion is a concurrent version control system which enables one
|lam, open mpi
or more users to collaborate in developing and maintaining a
hierarchy of files and directories while keeping a history of all
changes.  Subversion only stores the differences between versions,
instead of every complete file.  Subversion is intended to be a
compelling replacement for CVS.
|-
|-
|[http://pritch.bsd.uchicago.edu/software/STRAT.html STRAT]
|'''[[TopHat]]'''
|1.1
|1.1
|/share/apps/STRAT/1.1
|1.0.8
|STRAT is a companion program to structure. This is a structured association method, for use in association mapping, enabling valid case-control studies even in the presence of population structure.
|ngs-ccts 2.0.10
|-
|-
|[http://pritch.bsd.uchicago.edu/structure.html Structure]
|'''[[varianttools]]'''
|2.2.2
|1.0.1
|/share/apps/structure/2.2.2
|1.0
|Structure is software for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.
|
|-
|-
|[http://tophat.cbcb.umd.edu/ TopHat]
|'''[[vcftools]]'''
|1.0.8
|0.1.11
|/share/apps/tophat/1.0.8
|
|TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
|ngs-ccts
 
|-
TopHat is a collaborative effort between the University of Maryland Center for Bioinformatics and Computational Biology and the University of California, Berkeley Departments of Mathematics and Molecular and Cell Biology.
|'''[[VEGAS]]'''
 
|0.8
A TopHat tutorial is available here: http://tophat.cbcb.umd.edu/tutorial.html
|
 
|
The following Modules files should be loaded for this package, the tophat module will also load the bowtie module:
|-
<pre>
|'''[[velvet]]'''
module load tophat/tophat
|1.2.10
</pre>
|
 
|ngs-ccts
|-
|-
|[http://www.ks.uiuc.edu/Research/vmd/ VMD]
|'''[[VMD]]'''
|1.9.0
|1.8.6
|1.8.6
|/share/apps/vmd/vmd-1.8.6
|
|VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
|}
 
You'll need to use X forwarding to launch VMD (for example, on a Windows machine, X-Win32).


The following Modules files should be loaded for this package:
[[Category:Software]]
<pre>
module load vmd/vmd-1.8.6
</pre>
|-
|}

Latest revision as of 15:06, 6 October 2017

This page shows a list of installed modules on the Cheaha research computing system. If you don't find a particular package listed on this page, please send a request to cheaha support to request the software.

This list is not exhaustive and may not reflect the accurate current versions of the different software installed on the system. Please see the output of the module avail command for the official list of software modules installed on Cheaha.

Software modules installed on Cheaha

Software Latest Version Other Versions Remarks
AFNI AFNI_Jun_25_2013 AFNI_2011_12_21_1014 linux openmp 64, linux Xorg7 64
Affymetrix 1.14.3
Amber 10
ANNOVAR 2012Feb23 ngs-ccts 2013.09.11/2013.04.03
ANSYS 14.5 14.0
APBS 1.0
Aspera 2.4.7
Atlas 3.8
AutoDock 4.2.3
Birdsuite 1.5.5 1.5.3
Bowtie 0.9 0.10,0.12 ngs-ccts 2.1.0
bwa 0.6.2 0.5.10,0.5.9 ngs-ccts
cgatools 1.8.0 1.7.1,1.5.0 ngs-ccts
CHASE 1
cmake 2.8.10.2
CUDA 4
COMSOL 4.2
Cufflinks 0.9 ngs-ccts 2.1.1
DSSP 2.0.4
Eclipse 4.3.1
eigenstrat 2.0
EMAN2 2.02 ??
ENT 1.0.2
fastPHASE 1.4
FFTW 3.1.2 gnu/intel
FreeSurfer 5.3.0 4.5,5.2.0
FREGENE 2008
Fsl 5.0.6 4.1.6
Galaxy 1.0
gcc 4.8.1
genn
Gromacs 4.6.1 4,4.5 gnu/intel
GTOOL 0.6.7
HAPGEN 1.3.0
Haskell/GHC 6.10.4
HYPERWORKS 12.0
Illuminus 2
IMPUTE2 2.3.0 2.1.2,2.1.0, 2.0.3
JAGS 1.0 gnu
LAM-MPI 7.1 gnu/intel
LS-DYNA 9.7.1
MACH 1.0.16
MACS 1.3.6
Magma 5.2
Maq 0.7.1
MarthLab mosaik 0.9.891 gigabayes, pyrobayes
MATLAB R2013a R2009(a,b),R2010(a,b),R2011(a,b),R2012a DCS-128
MPICH 2 1.2 gnu/intel
mplayer 1.1.1
MrBayes 3.1.2 intel
MVAPICH 2 gnu
Namd 2.9 2.8,2.7,2.6 ibverbs
OpenMPI 1.6.4 1.2 gnu/intel
ParaView 3.12 3.4,3.6,3.8
PDT 3.19 3.14,3.17
PennCNV 2010May01
petsc 3.4.3
PHASE 2.1.1
PLINK 1.07 1.06,1.05
Python 2.7 2.6
R 3.0.1 2.6.2,2.7.2,2.8.1,2.9.0,2.9.2,2.11.1,2.12.2,2.14.2,2.15.0,2.15.3,3.0.0
RAxML 7.2.6
RNA pipeline 0.5.0 0.31
S.A.G.E. 6.2 6.0
SAMtools 0.1 ngs-ccts 0.1.19
ScaleMP 3.2.2 fftw optimized
SHRiMP 1.3 1.2
SOLAR 4.3.1
SPPARKS 30May11 07Aug09
Structure 2.2
tabix 0.2.6 ngs-ccts
TAU 2.22.2 2.21.1 lam, open mpi
TopHat 1.1 1.0.8 ngs-ccts 2.0.10
varianttools 1.0.1 1.0
vcftools 0.1.11 ngs-ccts
VEGAS 0.8
velvet 1.2.10 ngs-ccts
VMD 1.9.0 1.8.6
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