last updated: Wednesday, 18-May-2022 02:42:07 EDT

Lighthouse cluster software catalog

        


==============================================================================
Description:
Versions:     1.10.2
License:
Categories:
==============================================================================


Absoft Pro Fortran
==============================================================================
Description:  [SPECIAL LICENSE REQUIRED: contact arcts-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; 20.0.2
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
==============================================================================


Anaconda3
==============================================================================
Description:  Python Data Science Distribution
Versions:     2019.10; 2020.02; 2020.07; 2021.05
License:
Categories:   Python, Programming, Scripting, 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
==============================================================================


azcopy
==============================================================================
Description:  AzCopy is a command-line tool to copy data to and from Azure
              storage.
Versions:     10.9.0
License:      MIT License
Categories:   cloud, copy
==============================================================================


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; 3.21.3
License:      https://cmake.org/licensing/
Categories:   Utility, programming, compiler
==============================================================================


cuda
==============================================================================
Description:  CUDA compilers and libraries.
Versions:     10.0.130; 10.1.105; 10.2.89; 11.0.2; 11.2.1; 11.4.0; 11.5.1;
              8.0.61; 9.0.176; 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; 11.0-v8.0.2; 11.2-v8.1.0; 11.4-v8.2.2;
              11.5-v8.3.2; 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; 11.5.1; 8.0.61; 9.2.148
License:      http://docs.nvidia.com/cuda/eula
Categories:   CUDA, gpu, library, programming, Profiler
==============================================================================


DAGMC + OpenMC
==============================================================================
Description:  DAGMC is the Direct Accelerated Geometry Monte Carlo toolkit.
Versions:     1
License:
Categories:   Monte Carlo
==============================================================================


Dalton
==============================================================================
Description:  Dalton is an integrated suite of codes for electronic-
              structure calculations and materials modeling at the
              nanoscale.
Versions:     2018
License:      http://daltonprogram.org/download/
Categories:   electronic structure, materials modeling, ab initio quantum
              chemistry
==============================================================================


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
==============================================================================


FEKO
==============================================================================
Description:  [SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] Feko
              is a computational electromagnetics software.
Versions:     2021.1
License:      https://caen.engin.umich.edu/software/licensing/
Categories:   computational electromagnetics
==============================================================================


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
==============================================================================


gatk
==============================================================================
Description:  Toolkit for variant discovery and genotyping
Versions:     3.7
License:      Broad Institute Software License Agreement
Categories:   Bioinformatics
==============================================================================


Gaussian
==============================================================================
Description:  Gaussian is an electronic structure program.
Versions:     09-revD01; 16-revA03-avx; 16-revA03-avx2; 16-revA03-sse4_2
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; 3.1.0
License:      MIT (http://svn.osgeo.org/gdal/trunk/gdal/LICENSE.TXT)
Categories:   GIS, Geospatial, OGR
==============================================================================


GEOS
==============================================================================
Description:  OpenGIS Simple Features for SQL spatial predicate functions
              and spatial operators.
Versions:     3.8.1
License:      GNU LGPL v2.1
Categories:   GIS, Geometry, OSGeo
==============================================================================


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:     1.17.5
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
==============================================================================


HDF4
==============================================================================
Description:  HDF4 data libraries and utilities.
Versions:     4.2.15
License:      https://www.hdfgroup.org/products/licenses.html
Categories:   Utility, programming, library
==============================================================================


HDF5
==============================================================================
Description:  HDF5 data libraries and utilities.
Versions:     1.8.20; 1.10.6
License:      https://www.hdfgroup.org/products/licenses.html
Categories:   Utility, programming, library
==============================================================================


HELIOS
==============================================================================
Description:  [SPECIAL LICENSE REQUIRED: contact arcts-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 for on-campuse use only example of writing a
              module.
Versions:     1.2
License:      GPL
Categories:   Utility, example, template
==============================================================================


Image libraries
==============================================================================
Description:  Image libraries
Versions:     190711.1; 160610; 170303
License:      more than one
Categories:   libraries, programming, jpeg, gif, png, jbigkit, tiff,
              libwebp, lcms2, jasper
==============================================================================


impi
==============================================================================
Description:  Intel MPI runtime
Versions:     2018.3.222; 4.1.3; 2018.4.274
License:      GPL
Categories:   MPI, MPICH, programming
==============================================================================


Intel
==============================================================================
Description:  Intel compiler suite.
Versions:     14.0.4; 18.0.3; 18.0.5
License:      None provided
Categories:   Library, Development, Core
==============================================================================


julia
==============================================================================
Description:  The Julia Programming Language
Versions:     1.7.2
License:      MIT License
Categories:   Core
==============================================================================


Lahey Fortran
==============================================================================
Description:  [SPECIAL LICENSE REQUIRED: contact arcts-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
==============================================================================


LAMMPS
==============================================================================
Description:  LAMMPS is a classical molecular dynamics code that models an
              ensemble of particles.
Versions:     14May21; 27May21; 29Oct20; 30Nov20; 31Mar17; 7Aug19
License:      http://lammps.sandia.gov/doc/Section_intro.html#open-source-
              distribution
Categories:   molecular dynamics
==============================================================================


Launcher
==============================================================================
Description:  A framework for running large collections of serial or multi-
              threaded applications
Versions:     3.1.1; 3.5
License:      GPLv2
Categories:   Core
==============================================================================


Mathematica
==============================================================================
Description:  Mathematical and technical computing package.
Versions:     10.3.1; 11.1.0; 12.0.0; 12.2.0
License:      http://www.wolfram.com/legal/agreements/wolfram-
              mathematica.html
Categories:   Mathematics, symbolic algebra
==============================================================================


Matlab
==============================================================================
Description:  Matlab programming environment.
Versions:     R2017b; R2020a
License:
Categories:   Mathematics, programming, simulation
==============================================================================


mesa
==============================================================================
Description:  A 3D graphics library
Versions:     19.0.8
License:
Categories:   3D Graphics, OpenGL
==============================================================================


MKL
==============================================================================
Description:  Intel optimized BLAS/LAPACK libraries, also including FFT and
              other mathematical and statistical routines.
Versions:     11.1.2; 2018.0.3; 2018.0.4
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
==============================================================================


MPI for Python (mpi4py)
==============================================================================
Description:  Numerical libraries for use within Python.
Versions:     3.1.1
License:      https://github.com/mpi4py/mpi4py/blob/master/LICENSE.rst
Categories:   Programming, python, MPI, mpi4py
==============================================================================


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 arcts-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
==============================================================================


NumPy
==============================================================================
Description:  Numerical libraries for use within Python.
Versions:     1.21.2
License:      http://www.numpy.org/license.html
Categories:   Programming, numerical library, BLAS, LAPACK, python
==============================================================================


ompi
==============================================================================
Description:  OpenMPI implementation of the MPI protocol
Versions:     1.10.7; 3.1.4; 4.0.2; 3.1.6; 4.0.4; 4.0.6
License:      https://www.open-mpi.org/community/license.php
Categories:   Utility, Development, Core
==============================================================================


OpenFOAM
==============================================================================
Description:  OpenFOAM is a free, open source CFD software.
Versions:     v1712; v1906; v6-20190620
License:      http://www.openfoam.com/documentation/licencing.php
Categories:   CFD
==============================================================================


openmpi
==============================================================================
Description:  OpenMPI implementation of the MPI protocol
Versions:     1.10.7; 3.1.4; 4.0.2
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
==============================================================================


PGI compilers
==============================================================================
Description:  Compiler suite.
Versions:     19.10
License:      http://www.pgroup.com/doc/LICENSE.txt
Categories:   Compiler, development, debugger, profiler
==============================================================================


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
==============================================================================


PROJ
==============================================================================
Description:  PROJ is a generic coordinate transformation software.
Versions:     6.2.1
License:      MIT
Categories:   GIS, Library
==============================================================================


Python
==============================================================================
Description:  Python is a general purpose programming language
Versions:     3.7.3; 3.9.7
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; 3.6.3; 4.0.2; 4.1.0
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
==============================================================================


Rgeospatial
==============================================================================
Description:  A collection of R geospatial libraries
Versions:     2020-06-23
License:      GPL, https://www.r-project.org/Licenses/
Categories:   Statistics, graphics, big data, data science, geospatial,
              geography, spatial, map
==============================================================================


RStudio
==============================================================================
Description:  RStudio is an integrated development environment (IDE) for R
Versions:     1.2.1335; 1.4.1717
License:      AGPLv3
Categories:   R, statistics, graphics, data science, development,
              programming
==============================================================================


Rtidyverse
==============================================================================
Description:  R Tidyverse environment for statistical computing and graphics
Versions:     3.5.0; 4.0.2; 4.1.0
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
==============================================================================


SciPy
==============================================================================
Description:  Scientific libraries for use within Python.
Versions:     1.7.1
License:      http://www.scipy.org/scipylib/license.html
Categories:   Programming, python, solver
==============================================================================


Singularity
==============================================================================
Description:  Program for running containerized applications
Versions:     3.5.2; 3.6.1; 3.6.4; 3.7.3
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:     16; 17
License:      http://www.stata.com/order/end-user-license-agreement/
Categories:   Statistics, econometrics
==============================================================================


Stata/MP
==============================================================================
Description:  Statistical analysis software.
Versions:     16; 17
License:      http://www.stata.com/order/end-user-license-agreement/
Categories:   Statistics, econometrics
==============================================================================


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
==============================================================================


Tecplot 360 & Tecplot Focus
==============================================================================
Description:  Plotting and visualization software that gives full control
              over 2-D and 3-D plot parameters.
Versions:     2016; 2019; 2021
License:      file:///sw/coe/centos7/c/tecplot/2016/license.html
Categories:   plotting, visualization
==============================================================================


TensorFlow
==============================================================================
Description:  Machine learning platform for use within Python.
Versions:     2.1.3; 2.3.2; 2.5.0
License:      Apache License 2.0
Categories:   Programming, machine learning library, python
==============================================================================


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


use.own
==============================================================================
Description:  Module to add personal module directory to module path.
Versions:     1.0
License:      None
Categories:   utility
==============================================================================


VASP
==============================================================================
Description:  [SPECIAL LICENSE REQUIRED: contact arcts-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
==============================================================================


wine
==============================================================================
Description:  Wine is a compatability layer capable of running Windows apps
              on unix systems.
Versions:     3.0.3
License:
Categories:
==============================================================================


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