last updated: Thursday, 12-Dec-2019 15:13:34 EST

Armis2 cluster software catalog

        

Absoft Pro Fortran
==============================================================================
Description:  [SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu]
              Absoft Pro Fortran Compiler
Versions:     18.0.2
License:      http://www.absoft.com/literature/Absoftlicense.pdf
Categories:   fortran, compiler, f95/f90
==============================================================================


AFNI
==============================================================================
Description:  AFNI suite of MRI neuroimaging tools.
Versions:     18.0.27
License:      https://afni.nimh.nih.gov/legal_info
Categories:   fMRI, DTI, MRI, neuroimaging, neuroscience
==============================================================================


Allinea Forge
==============================================================================
Description:  Parallel debugging and profiling tools, DDT and MAP.
Versions:     19.0.4
License:      Not available
Categories:   Programming, profiler, debugger, performance
==============================================================================


Allinea Reports
==============================================================================
Description:  Parallel profiling tool.
Versions:     19.0.4
License:      Not available
Categories:   Programming, profiler, performance
==============================================================================


amber
==============================================================================
Description:  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.
Versions:     18
License:      Campus Agreement
Categories:   Computational Chemistry, Molecular Dynamics
==============================================================================


AMPL
==============================================================================
Description:  AMPL algebraic modelling language.
Versions:     20160714
License:      http://ampl.com/buy-ampl-terms-and-conditions/
Categories:   Optimization, linear programming, algebraic modelling
==============================================================================


Anaconda Python 3
==============================================================================
Description:  Python 3 distribution for scientific computing, including
              accelerated commercial versions of several Python packages.
Versions:     5.2
License:      Academic Cluster License,
              https://docs.continuum.io/anaconda/eula
Categories:   Python, numpy, scipy, matplotlib, IPython, Jupyter
==============================================================================


ANTs
==============================================================================
Description:  ANTs MRI image registration program
Versions:     2.1.0
License:      ANTs is Apache License 2.0
Categories:   image processing, image registration, fMRI, neuroimaging
==============================================================================


ANTsR
==============================================================================
Description:  R with ANTsR available via site libraries.
Versions:     3.3.3
License:      ANTsR is Apache License 2.0 and R is GPL,
              https://www.r-project.org/Licenses/
Categories:   Statistics, graphics, big data, data science, ANTs, image
              processing, image registration, fMRI
==============================================================================


BEDOPS
==============================================================================
Description:  BEDOPS is an open-source command-line toolkit that performs
              highly efficient and scalable Boolean and other set
              operations, statistical calculations, archiving, conversion
              and other management of genomic data of arbitrary scale. Tasks
              can be easily split by chromosome for distributing whole-
              genome analyses across a computational cluster.
Versions:     2.4.26
License:      GNU GPL v2
Categories:   Bioinformatics, Genomics
==============================================================================


bedtools
==============================================================================
Description:  a swiss-army knife of tools for a wide-range of genomics
              analysis tasks.
Versions:     2.20.1; 2.25.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


Boost
==============================================================================
Description:  Boost C++ library collection.
Versions:     1.67.0
License:      http://www.boost.org/users/license.html
Categories:   Programming, C++, library
==============================================================================


bowtie2
==============================================================================
Description:  Bowtie 2 is an ultrafast and memory-efficient tool for
              aligning sequencing reads to long reference sequences.
Versions:     2.1.0; 2.2.9; 2.3.1; 2.3.2; 2.3.3; 2.3.4.3
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


bwa
==============================================================================
Description:  BWA is a software package for mapping low-divergent sequences
              against a large reference genome, such as the human genome.
Versions:     0.5.9; 0.7.15; 0.7.3a; 0.7.8
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


CMake
==============================================================================
Description:  CMake cross-platform make system.
Versions:     3.14.3
License:      https://cmake.org/licensing/
Categories:   Utility, programming, compiler
==============================================================================


cuda
==============================================================================
Description:  CUDA compilers and libraries.
Versions:     10.0.130; 10.1.105; 8.0.61; 9.2.148
License:      http://docs.nvidia.com/cuda/eula/index.html
Categories:   CUDA, gpu, library, programming
==============================================================================


cudnn
==============================================================================
Description:  cuDNN libraries.
Versions:     10.0-v7.6; 10.1-v7.6; 8.0-v7.1
License:      http://docs.nvidia.com/cuda/eula
Categories:   CUDA, gpu, library, programming, cuDNN, deep learning, neural
              network
==============================================================================


cufflinks
==============================================================================
Description:  Transcriptome assembly and differential expression analysis
              for RNA-Seq.
Versions:     2.1.1; 2.2.0; 2.2.1
License:      Cufflinks is provided under the OSI-approved Boost License
Categories:   Bioinformatics
==============================================================================


CUPTI
==============================================================================
Description:  CUDA Profiler Tools Interface
Versions:     10.1.105; 8.0.61; 9.2.148
License:      http://docs.nvidia.com/cuda/eula
Categories:   CUDA, gpu, library, programming, Profiler
==============================================================================


eXpress
==============================================================================
Description:  eXpress is a streaming tool for quantifying the abundances of
              a set of target sequences from sampled subsequences.
Versions:     1.5.1
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


fastqc
==============================================================================
Description:  A quality control tool for high throughput sequence data.
Versions:     0.10.1; 0.11.5
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


FFMPEG
==============================================================================
Description:  FFMPEG is a complete, cross-platform solution to record,
              convert and stream audio and video.
Versions:     3.0.2; 3.2.4
License:      https://ffmpeg.org/legal.html
Categories:   audio, video, codec, transcoder
==============================================================================


fftw
==============================================================================
Description:  Libraries for computation of discrete Fourier transform.
Versions:     3.3.7
License:      http://www.fftw.org/fftw3_doc/License-and-Copyright.html
Categories:   Library, Development, Core
==============================================================================


FLEXlm
==============================================================================
Description:  FLEXlm utility programs.
Versions:     11.11.1.2
License:      None provided
Categories:   Utility
==============================================================================


FreeSurfer
==============================================================================
Description:  FreeSurfer MRI processing and analysis software.
Versions:     6.0.0
License:      http://freesurfer.net/fswiki/FreeSurferSoftwareLicense
Categories:   MRI, neuroimaging, neuroscience
==============================================================================


FSL
==============================================================================
Description:  FSL suite of MRI neuroimaging tools.
Versions:     5.0.11
License:      http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
Categories:   fMRI, DTI, neuroimaging, neuroscience
==============================================================================


g95
==============================================================================
Description:  G95 - f95/f90 fortran compiler
Versions:     0.94
License:      http://www.gnu.org/licenses/gpl.html
Categories:   fortran, compiler
==============================================================================


Gaussian
==============================================================================
Description:  Gaussian is an electronic structure program.
Versions:     09-revD01; 16-revA03-avx2; 16revA03
License:      Academic, noncommercial research and instructional use only.
Categories:   electronic structure, molecular
==============================================================================


gcc
==============================================================================
Description:  GNU compiler suite
Versions:     4.8.5; 8.2.0
License:      GPL
Categories:   Compiler, programming, development
==============================================================================


GDAL
==============================================================================
Description:  GDAL is a translator library for raster and vector geospatial
              data formats.
Versions:     2.1.4; 2.3.2
License:      MIT (http://svn.osgeo.org/gdal/trunk/gdal/LICENSE.TXT)
Categories:   GIS, Geospatial, OGR
==============================================================================


git
==============================================================================
Description:  Git version control software
Versions:     2.14.2
License:      GPL version 2
Categories:   Utility, development, version control
==============================================================================


GMP
==============================================================================
Description:  GNU multiprecision arithmetic library
Versions:     6.1.2
License:      GPL
Categories:   Programming, library, mathematics
==============================================================================


Go
==============================================================================
Description:  Go is an open source programming language that makes it easy
              to build simple, reliable, and efficient software.
Versions:     1.11
License:      https://golang.org/LICENSE?m=text
Categories:   Go, Programming
==============================================================================


GSL
==============================================================================
Description:  GNU scientific libraries
Versions:     2.1
License:      GPL
Categories:   Programming, library, mathematics
==============================================================================


Gurobi
==============================================================================
Description:  Gurobi optimization problem solver.
Versions:     6.5.2
License:      http://www.gurobi.com/pdfs/eula/eula-gurobi.pdf
Categories:   Optimization, linear programming
==============================================================================


HDF5
==============================================================================
Description:  HDF5 data libraries and utilities.
Versions:     1.8.20
License:      https://www.hdfgroup.org/products/licenses.html
Categories:   Utility, programming, library
==============================================================================


HELIOS
==============================================================================
Description:  [SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu]
              HELIOS Generalized Geometry Lattice Analysis package. Includes
              Casmo and Simulate from teh Studsvik suite.
Versions:     1.12
License:      N/A
Categories:   Geometry Lattice Analysis, hexagonal VVER reactors, non-LWR
              lattices
==============================================================================


Hello
==============================================================================
Description:  Hello world example of writing a module.
Versions:     1.2
License:      GPL
Categories:   Utility, example, template
==============================================================================


Image libraries
==============================================================================
Description:  Image libraries
Versions:     160610; 170303
License:      more than one
Categories:   libraries, programming, jpeg, gif, png
==============================================================================


impi
==============================================================================
Description:  Intel MPI runtime
Versions:     2018.3.222; 4.1.3
License:      GPL
Categories:   MPI, MPICH, programming
==============================================================================


Intel
==============================================================================
Description:  Intel compiler suite.
Versions:     14.0.4; 18.0.3
License:      None provided
Categories:   Library, Development, Core
==============================================================================


Lahey Fortran
==============================================================================
Description:  [SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu]
              Lahey Fortran - f95/f90 fortran compiler
Versions:     8.1b
License:      http://www.lahey.com/docs/lfpro73help/f95gslicense.htm
Categories:   fortran, compiler, f95/f90
==============================================================================


Launcher
==============================================================================
Description:  A simple utility for executing multiple sequential or multi-
              threaded applications in a single multi-node batch job
Versions:     3.1.1
License:      MIT
Categories:   Utility, batch-processing, serial, high-throughput
==============================================================================


Mathematica
==============================================================================
Description:  Mathematical and technical computing package.
Versions:     10.3.1; 11.1.0; 12.0.0
License:      http://www.wolfram.com/legal/agreements/wolfram-
              mathematica.html
Categories:   Mathematics, symbolic algebra
==============================================================================


Matlab
==============================================================================
Description:  Matlab programming environment.
Versions:     R2017b
License:
Categories:   Mathematics, programming, simulation
==============================================================================


MKL
==============================================================================
Description:  Intel optimized BLAS/LAPACK libraries, also including FFT and
              other mathematical and statistical routines.
Versions:     11.1.2; 2018.0.3
License:      https://software.intel.com/sites/default/files/managed/86/1d/M
              aster_EULA_for_Intel_Sw_Development_Products.pdf
Categories:   Library, Development, Core, BLAS, LAPACK
==============================================================================


MPC
==============================================================================
Description:  GNU C library for the arithmetic of complex numbers with
              arbitrarily high precision and correct rounding of the result.
Versions:     1.1.0
License:      GPL
Categories:   Programming, library, mathematics
==============================================================================


MPFR
==============================================================================
Description:  GNU multiprecision arithmetic library
Versions:     4.0.1
License:      GPL
Categories:   Programming, library, mathematics
==============================================================================


MRIcron
==============================================================================
Description:  Image viewer for NIfTI images and DICOM conversion
Versions:     30apr2016
License:      Standard BSD 2-Clause license
Categories:   fMRI, neuroimaging, DICOM, NIfTI
==============================================================================


MRtrix
==============================================================================
Description:  MRtrix provides a set of tools to perform various advanced
              diffusion MRI analyses.
Versions:     3.0_RC3
License:      Mozill Public License, http://mozilla.org/MPL/2.0/
Categories:   fMRI, diffusion-weighted MRI, tractography, neuroimaging
==============================================================================


nagf95
==============================================================================
Description:  [SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu]
              NAGWARE - f95/f90 fortran compiler
Versions:     6.1-6120; 6.2-6214
License:      file:///sw/coe/centos7/c/nagf95/6.1-6120/lic_agr.txt
Categories:   fortran, compiler
==============================================================================


ncbi-blast
==============================================================================
Description:  Basic Local Alignment Search Tool (BLAST) is the most widely
              used sequence similarity tool.
Versions:     2.2.29; 2.5.0
License:      United States Government Work under the terms of the United
              States Copyright Act
Categories:   Bioinformatics
==============================================================================


NCL
==============================================================================
Description:  NCAR command language for visualization.
Versions:     6.4.0
License:      http://www2.ucar.edu/terms-of-use
Categories:   Visualization, NetCDF, HDF5
==============================================================================


NetCDF
==============================================================================
Description:  Libraries for creating and manipulating NetCDF files.
Versions:     4.6.0
License:
Categories:   Library, Development, Core
==============================================================================


ompi
==============================================================================
Description:  OpenMPI implementation of the MPI protocol
Versions:     1.10.7; 3.1.4
License:      https://www.open-mpi.org/community/license.php
Categories:   Utility, Development, Core
==============================================================================


openmpi
==============================================================================
Description:  OpenMPI implementation of the MPI protocol
Versions:     1.10.7; 3.1.4
License:      https://www.open-mpi.org/community/license.php
Categories:   Utility, Development, Core
==============================================================================


perl-modules/1.0
==============================================================================
Description:  Perl addin modules for use with Perl version 5.16.3.
Versions:     1.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


picard-tools
==============================================================================
Description:  A set of tools for working with high-throughput sequencing
              data
Versions:     1.76; 1.79; 2.18.17; 2.3.0; 2.4.1
License:      MIT License, Apache License V2.0
Categories:   Bioinformatics
==============================================================================


Python
==============================================================================
Description:  Python is a general purpose programming language
Versions:     3.7.3
License:      https://docs.python.org/3/license.html
Categories:   Programming, language
==============================================================================


R
==============================================================================
Description:  R environment for statistical computing and graphics
Versions:     3.5.0; 3.5.1
License:      GPL, https://www.r-project.org/Licenses/
Categories:   Statistics, graphics, big data, data science
==============================================================================


r-biomed-libs
==============================================================================
Description:  R libraries for bioinformatics, genomics, and sequencing.
Versions:     3.5.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


RStudio
==============================================================================
Description:  RStudio is an integrated development environment (IDE) for R
Versions:     1.2.1335
License:      AGPLv3
Categories:   R, statistics, graphics, data science, development,
              programming
==============================================================================


Rtidyverse
==============================================================================
Description:  R Tidyverse environment for statistical computing and graphics
Versions:     3.5.0
License:      GPL, https://www.r-project.org/Licenses/
Categories:   Statistics, graphics, big data, data science, tidyverse
==============================================================================


salmon
==============================================================================
Description:  Salmon is a tool for wicked-fast transcript quantification
              from RNA-seq data.
Versions:     0.11.3; 0.8.2; 0.9.1
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


samtools
==============================================================================
Description:  SAM (Sequence Alignment/Map) format is a generic format for
              storing large nucleotide sequence alignments.
Versions:     0.1.18; 0.1.19; 1.2; 1.5
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


SAS
==============================================================================
Description:  SAS statistical system software.
Versions:     9.4
License:      Not available
Categories:   Statitics, econometrics
==============================================================================


Singularity
==============================================================================
Description:  Program for running containerized applications
Versions:     3.4.1
License:      https://github.com/sylabs/singularity/blob/master/LICENSE.md
Categories:   Container, docker, reproducible research
==============================================================================


STAR
==============================================================================
Description:  Spliced Transcripts Alignment to a Reference
Versions:     2.5.2a
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


Stata
==============================================================================
Description:  Statistical analysis software.
Versions:     14; 15; 16
License:      http://www.stata.com/order/end-user-license-agreement/
Categories:   Statistics, econometrics
==============================================================================


Stata/MP
==============================================================================
Description:  Statistical analysis software.
Versions:     14; 15; 16
License:      http://www.stata.com/order/end-user-license-agreement/
Categories:   Statistics, econometrics
==============================================================================


subread
==============================================================================
Description:  a tool kit for processing next-gen sequencing data
Versions:     1.5.0; 1.6.1
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


szip
==============================================================================
Description:  Szip is a compression library used with HDF5.
Versions:     2.1.1
License:      https://www.hdfgroup.org/doc_resource/SZIP/
Categories:   Utility, compression
==============================================================================


trimmomatic
==============================================================================
Description:  Trimmomatic: A flexible read trimming tool for Illumina NGS
              data
Versions:     0.36
License:      GNU GPL v3
Categories:   Bioinformatics, Sequencing
==============================================================================


VASP
==============================================================================
Description:  [SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu]
              VASP, The Vienna Ab initio simulation package, a plane wave
              electronic structure code.
Versions:     5.4.1.05Feb16.p2.b; 5.4.4.18Apr17; 5.4.4.18Apr17.p1;
              5.4.4.18Apr17.vaspsol.170729; old-4.6.36Feb09;
              old-5.2.12.11Nov2011; old-5.3.2.13Sep2012;
              old-5.3.3.18Dec2012; old-5.3.5.31Mar2014;
              old-5.3.5.31Mar2014wannier90v12
License:      https://www.vasp.at/index.php/faqs
Categories:   electronic structure code, molecular dynamics
==============================================================================


Yasm
==============================================================================
Description:  Yasm assembler.
Versions:     1.3.0
License:      https://github.com/yasm/yasm/blob/master/BSD.txt
Categories:   assembler, programming
==============================================================================