last updated: Saturday, 20-Apr-2024 00:28:05 EDT

Lighthouse cluster software catalog

        

Abaqus
==============================================================================
Description:  Abaqus FEA product suite for engineering problems.
Versions:     2022
License:      Non-commercial research, Academic Institution License
              Agreement
Categories:   FEA, dynamic vibration, impact/crash, thermal coupling
==============================================================================


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; 22.2.07
License:      https://afni.nimh.nih.gov/legal_info
Categories:   fMRI, DTI, MRI, neuroimaging, neuroscience
==============================================================================


AMPL
==============================================================================
Description:  AMPL algebraic modeling language.
Versions:     20220703
License:      http://ampl.com/buy-ampl-terms-and-conditions/
Categories:   Optimization, linear programming, algebraic modeling
==============================================================================


Anaconda3
==============================================================================
Description:  Python Data Science Distribution
Versions:     2023.03; 2021.11
License:      https://www.anaconda.com/eula-anaconda-individual-edition
Categories:   Python, Programming, Scripting, numpy, scipy, matplotlib,
              ipython, jupyter
==============================================================================


angsd
==============================================================================
Description:  Angsd is a program for analysing NGS data.
Versions:     0.935
License:      N/A
Categories:   N/A
==============================================================================


ANSYS
==============================================================================
Description:  ANSYS is a finite element simulation tool for multiphysics
              simulations.
Versions:     21.2
License:      Academic Research
Categories:   CFD, FEM, finite element, multiphysics
==============================================================================


ANSYS EM
==============================================================================
Description:  ANSYS EM: HFSS and Maxwell
Versions:     21.2
License:      Academic Research
Categories:   EM, CEM, HFSS, Maxwell
==============================================================================


ANTs
==============================================================================
Description:  ANTs MRI image registration program
Versions:     2.4.1
License:      ANTs is Apache License 2.0
Categories:   image processing, image registration, fMRI, neuroimaging
==============================================================================


archivetar
==============================================================================
Description:  Parallel archive manipulation tool
Versions:     0.15.6; 0.16.0
License:      https://github.com/brockpalen/archivetar/blob/master/LICENSE
Categories:   Utility
==============================================================================


ARM Forge
==============================================================================
Description:  Parallel debugging and profiling tools, DDT and MAP.
Versions:     21.1.3
License:      Not available
Categories:   Programming, profiler, debugger, performance
==============================================================================


aws-cli
==============================================================================
Description:  AWS command line interface
Versions:     False
License:      https://aws.amazon.com/terms/
Categories:   Amazon, AWS, utility
==============================================================================


bamtools
==============================================================================
Description:  C++ API & command-line toolkit for working with BAM data.
Versions:     2.5.1; 2.5.2
License:      N/A
Categories:   N/A
==============================================================================


bcftools
==============================================================================
Description:  BCFtools is a set of utilities that manipulate variant calls
              in the Variant Call Format (VCF) and its binary counterpart
              BCF. All commands work transparently with both VCFs and BCFs,
              both uncompressed and BGZF-compressed.
Versions:     1.12
License:      N/A
Categories:   N/A
==============================================================================


bcl-convert
==============================================================================
Description:  Converts the Binary Base Call (BCL) files produced by Illumina
              sequencing systems to FASTQ files.
Versions:     4.2.4
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


bcl2fastq2
==============================================================================
Description:  The bcl2fastq2 Conversion Software converts base call (BCL)
              files from a sequencing run into FASTQ files.
Versions:     2.20.0.422
License:      N/A
Categories:   N/A
==============================================================================


beast1
==============================================================================
Description:  BEAST is a cross-platform program for Bayesian analysis of
              molecular sequences using MCMC.
Versions:     1.10.4
License:      N/A
Categories:   N/A
==============================================================================


bedtools2
==============================================================================
Description:  Collectively, the bedtools utilities are a swiss-army knife of
              tools for a wide-range of genomics analysis tasks. The most
              widely-used tools enable genome arithmetic: that is, set
              theory on the genome.
Versions:     2.25.0; 2.30.0
License:      N/A
Categories:   N/A
==============================================================================


blast-plus
==============================================================================
Description:  Basic Local Alignment Search Tool.
Versions:     2.12.0
License:      N/A
Categories:   N/A
==============================================================================


blat
==============================================================================
Description:  BLAT (BLAST-like alignment tool) is a pairwise sequence
              alignment algorithm.
Versions:     35
License:      N/A
Categories:   N/A
==============================================================================


Boost
==============================================================================
Description:  Boost C++ library collection.
Versions:     1.78.0
License:      http://www.boost.org/users/license.html
Categories:   Programming, C++, library
==============================================================================


bowtie
==============================================================================
Description:  Bowtie is an ultrafast, memory-efficient short read aligner
              for short DNA sequences (reads) from next-gen sequencers.
Versions:     1.3.0
License:      N/A
Categories:   N/A
==============================================================================


bowtie2
==============================================================================
Description:  Bowtie 2 is an ultrafast and memory-efficient tool for
              aligning sequencing reads to long reference sequences
Versions:     2.4.1; 2.4.2
License:      N/A
Categories:   N/A
==============================================================================


Bridger Assembler
==============================================================================
Description:  Bridger is an efficient de novo trascriptome assembler for
              RNA-Seq data.
Versions:     2014.12.01
License:      GNU GENERAL PUBLIC LICENSE
Categories:   Bioinformatics, Genomics, Healthcare, big data
==============================================================================


bwa
==============================================================================
Description:  Burrow-Wheeler Aligner for pairwise alignment between DNA
              sequences.
Versions:     0.7.15; 0.7.17
License:      N/A
Categories:   N/A
==============================================================================


canu
==============================================================================
Description:  A single molecule sequence assembler for genomes large and
              small.
Versions:     2.2
License:      N/A
Categories:   N/A
==============================================================================


cap3
==============================================================================
Description:  CAP3 is DNA Sequence Assembly Program
Versions:     2015-02-11
License:      N/A
Categories:   N/A
==============================================================================


cellpose
==============================================================================
Description:  cellpose is an anatomical segmentation algorithm written in
              Python 3.
Versions:     2.1.1
License:      https://github.com/MouseLand/cellpose/blob/main/LICENSE
Categories:   Biology, deep-learning, biomedical, cell segmentation, image
              analysis
==============================================================================


cellranger
==============================================================================
Description:  Cell Ranger is a set of analysis pipelines that process
              Chromium single-cell RNA-seq output
Versions:     7.1.0; 7.2.0; 8.0.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


cellrangerARC
==============================================================================
Description:  a set of analysis pipelines that process Chromium Single Cell
              Multiome ATAC + Gene Expression sequencing data
Versions:     2.0.2
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


cellrangerATAC
==============================================================================
Description:  a set of analysis pipelines that process Chromium Single Cell
              ATAC data
Versions:     2.1.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


clustal-omega
==============================================================================
Description:  Clustal Omega: the last alignment program you'll ever need.
Versions:     1.2.4
License:      N/A
Categories:   N/A
==============================================================================


CMake
==============================================================================
Description:  CMake cross-platform make system.
Versions:     3.22.2; 3.26.3
License:      https://cmake.org/licensing/
Categories:   Utility, programming, compiler
==============================================================================


code-server
==============================================================================
Description:  Run VS Code on any machine anywhere and access it in the
              browser.
Versions:     4.8.3
License:      MIT
Categories:   file management, software development, scripting, IDE.
==============================================================================


cuda
==============================================================================
Description:  CUDA compilers and libraries.
Versions:     10.2.89; 11.2.2; 11.3.0; 11.5.1; 11.6.2; 11.7.1; 11.8.0;
              12.1.1
License:      http://docs.nvidia.com/cuda/eula/index.html
Categories:   CUDA, gpu, library, programming
==============================================================================


cudnn
==============================================================================
Description:  cuDNN libraries.
Versions:     10.2-v8.3.1; 11.2-v8.1.1; 11.3-v8.2.1; 11.5-v8.3.1;
              11.6-v8.4.1; 11.7-v8.7.0; 11.8-v8.7.0; 12.1-v8.9.0
License:      http://docs.nvidia.com/cuda/eula
Categories:   CUDA, gpu, library, programming, cuDNN, deep learning, neural
              network
==============================================================================


cufflinks
==============================================================================
Description:  Cufflinks assembles transcripts, estimates their abundances,
              and tests for differential expression and regulation in RNA-
              Seq samples.
Versions:     2.2.1
License:      N/A
Categories:   N/A
==============================================================================


CUPTI
==============================================================================
Description:  CUDA Profiler Tools Interface
Versions:     10.2.89; 11.2.2; 11.3.0; 11.5.1; 11.6.2; 11.7.1; 11.8.0;
              12.1.1
License:      http://docs.nvidia.com/cuda/eula
Categories:   CUDA, gpu, library, programming, Profiler
==============================================================================


delly2
==============================================================================
Description:  Delly2 is an integrated structural variant prediction method
              that can discover, genotype and visualize deletions, tandem
              duplications, inversions and translocations at single-
              nucleotide resolution in short-read massively parallel
              sequencing data..
Versions:     0.9.1
License:      N/A
Categories:   N/A
==============================================================================


Eigen
==============================================================================
Description:  Linear algebra template library
Versions:     3.4.0
License:      https://eigen.tuxfamily.org/index.php
Categories:   Linear algebra, numerical, development, library
==============================================================================


fastqc
==============================================================================
Description:  A quality control tool for high throughput sequence data.
Versions:     0.11.5; 0.11.9; 0.12.1
License:      N/A
Categories:   N/A
==============================================================================


FEKO
==============================================================================
Description:  [SPECIAL LICENSE REQUIRED: contact arc-support@umich.edu] Feko
              is a computational electromagnetics software.
Versions:     2021.2; 2022.1
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:     4.4.2; 5.1.2; 6.0.0
License:      https://ffmpeg.org/legal.html
Categories:   audio, video, codec, transcoder
==============================================================================


fftw
==============================================================================
Description:  Libraries for computation of discrete Fourier transform.
Versions:     3.3.10
License:      http://www.fftw.org/fftw3_doc/License-and-Copyright.html
Categories:   Library, Development, Core
==============================================================================


figtree
==============================================================================
Description:  FigTree is designed as a graphical viewer of phylogenetic
              trees and as a program for producing publication-ready
              figures. As with most of my programs, it was written for my
              own needs so may not be as polished and feature-complete as a
              commercial program. In particular it is designed to display
              summarized and annotated trees produced by BEAST.
Versions:     1.4.4
License:      N/A
Categories:   N/A
==============================================================================


FreeSurfer
==============================================================================
Description:  FreeSurfer MRI processing and analysis software.
Versions:     7.2.0
License:
              https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLi
              cense
Categories:   MRI, neuroimaging, neuroscience
==============================================================================


FSL
==============================================================================
Description:  FSL suite of MRI neuroimaging tools.
Versions:     6.0.5.2
License:      http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
Categories:   fMRI, DTI, neuroimaging, neuroscience
==============================================================================


gatk
==============================================================================
Description:  Toolkit for variant discovery and genotyping
Versions:     3.7; 4.1.0.0; 4.2.2.0
License:      Broad Institute Software License Agreement
Categories:   Bioinformatics
==============================================================================


Gaussian
==============================================================================
Description:  Gaussian is an electronic structure program.
Versions:     09-revD01; 16-revA03-avx2; 16-revC01-avx2
License:      Academic, noncommercial research and instructional use only.
Categories:   electronic structure, molecular
==============================================================================


gcc
==============================================================================
Description:  GNU compiler suite
Versions:     10.3.0; 11.2.0; 13.2.0
License:      GPL
Categories:   Compiler, programming, development
==============================================================================


GDAL
==============================================================================
Description:  GDAL is a translator library for raster and vector geospatial
              data formats.
Versions:     3.5.1; 3.8.3
License:      https://gdal.org/license.html
Categories:   GIS, geospatial, raster, vector, graphics
==============================================================================


GEOS
==============================================================================
Description:  OpenGIS Simple Features for SQL spatial predicate functions
              and spatial operators.
Versions:     3.10.2; 3.12.1
License:      GNU LGPL v2.1
Categories:   GIS, Geometry, OSGeo
==============================================================================


git
==============================================================================
Description:  Git version control software
Versions:     2.39.1
License:      GPL version 2
Categories:   Utility, development, version control
==============================================================================


git-annex
==============================================================================
Description:  Manage large files with git, without storing the file contents
              in git
Versions:     10.20220928
License:      AGPL version 3.0
Categories:   Utility, development, version control, file management
==============================================================================


globus-cli
==============================================================================
Description:  The CLI provides an interface to Globus services from the
              shell, and is suited to both interactive and simple scripting
              use cases.
Versions:     3.4.0
License:      N/A
Categories:   Data movement
==============================================================================


Go
==============================================================================
Description:  The Go programming language is an open source project to make
              programmers more productive.
Versions:     1.18
License:      https://go.dev/LICENSE?m=text
Categories:   Go, Programming, golang
==============================================================================


GSL
==============================================================================
Description:  GNU scientific libraries
Versions:     2.7
License:      GPL
Categories:   Programming, library, mathematics
==============================================================================


gst-libav
==============================================================================
Description:  GStreamer plugin for the libav* library.
Versions:     1.16.1
License:      https://github.com/GStreamer/gst-libav?tab=LGPL-2.1-1-ov-
              file#readme
Categories:   multimedia
==============================================================================


Gurobi
==============================================================================
Description:  Gurobi optimization problem solver.
Versions:     10.0.2; 9.5.1
License:      http://www.gurobi.com/pdfs/eula/eula-gurobi.pdf
Categories:   Optimization, linear programming
==============================================================================


HDF5
==============================================================================
Description:  HDF5 data libraries and utilities.
Versions:     1.10.8; 1.8.22
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; 1.12-sing; 1.13
License:      N/A
Categories:   Geometry Lattice Analysis, hexagonal VVER reactors, non-LWR
              lattices
==============================================================================


hisat2
==============================================================================
Description:  HISAT2 is a fast and sensitive alignment program for mapping
              next-generation sequencing reads (whole-genome, transcriptome,
              and exome sequencing data) against the general human
              population (as well as against a single reference genome).
Versions:     2.2.0
License:      N/A
Categories:   N/A
==============================================================================


homer
==============================================================================
Description:  Software for motif discovery and next generation sequencing
              analysis
Versions:     4.11.1
License:      N/A
Categories:   N/A
==============================================================================


HPC compilers
==============================================================================
Description:  Compiler suite.
Versions:     22.3
License:      https://docs.nvidia.com/hpc-sdk/eula/hpc-sdk-ea-eula.pdf
Categories:   Compiler, development, debugger, profiler
==============================================================================


htslib
==============================================================================
Description:  C library for high-throughput sequencing data formats.
Versions:     1.13; 1.9
License:      N/A
Categories:   N/A
==============================================================================


igv
==============================================================================
Description:  The Integrative Genomics Viewer (IGV) is a high-performance
              visualization tool for interactive exploration of large,
              integrated genomic datasets. It supports a wide variety of
              data types, including array-based and next-generation sequence
              data, and genomic annotations.
Versions:     2.8.9
License:      N/A
Categories:   N/A
==============================================================================


ilastik
==============================================================================
Description:  Interactive learning and segmentation toolkit.
Versions:     1.4.0
License:      https://www.ilastik.org/license.html
Categories:   Machine learning, image classification, image analysis.
==============================================================================


Image libraries
==============================================================================
Description:  Image libraries
Versions:     220318.1; 220318
License:      more than one
Categories:   libraries, programming, jpeg, gif, png, jbigkit, tiff,
              libwebp, lcms2, jasper, ImageMagick
==============================================================================


imagemagick
==============================================================================
Description:  ImageMagick is a software suite to create, edit, compose, or
              convert bitmap images.
Versions:     7.1.0-33
License:      N/A
Categories:   N/A
==============================================================================


impi
==============================================================================
Description:  Intel MPI runtime
Versions:     2021.5.1; 2018.4.274
License:      GPL
Categories:   MPI, MPICH, programming
==============================================================================


impute2
==============================================================================
Description:  IMPUTE2 is a genotype imputation and haplotype phasing program
              based on ideas from Howie et al. 2009.
Versions:     2.3.2
License:      N/A
Categories:   N/A
==============================================================================


Intel
==============================================================================
Description:  Intel compiler suite.
Versions:     18.0.5; 2022.1.2
License:      None provided
Categories:   Library, Development, Core
==============================================================================


itk
==============================================================================
Description:  The Insight Toolkit (ITK) is an open-source, cross-platform
              toolkit for N-dimensional scientific image processing,
              segmentation, and registration.
Versions:     5.2.1
License:      N/A
Categories:   N/A
==============================================================================


ITK
==============================================================================
Description:  ITK is an open-source system for medical image processing.
Versions:     5.2.1; 5.3.0
License:      https://software.intel.com/en-us/license/intel-simplified-
              software-license
Categories:   Library, development, image processing, MRI, NIfTI
==============================================================================


JAGS
==============================================================================
Description:  JAGS is Just Another Gibbs Sampler. It is a program for
              analysis of Bayesian hierarchical models.
Versions:     4.3.0
License:      GNU GPL v2
Categories:   Bayesian, Markov, MCMC
==============================================================================


joe
==============================================================================
Description:  JOE editor.
Versions:     4.6
License:      https://joe-editor.sourceforge.io/
Categories:   Editor, development, utility
==============================================================================


Julia
==============================================================================
Description:  Julia is a high-level, high-performance dynamic language for
              technical computing. The main homepage for Julia can be found
              at julialang.org.
Versions:     1.10.2; 1.7.2
License:      MIT Licenses
Categories:   Programming
==============================================================================


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


LAPACK
==============================================================================
Description:  LAPACK is written in Fortran 90 and provides routines for
              solving systems of simultaneous linear equations, least-
              squares solutions of linear systems of equations, eigenvalue
              problems, and singular value problems.
Versions:     3.10.1
License:      http://www.netlib.org/lapack/LICENSE.txt
Categories:   Libraries
==============================================================================


Launcher
==============================================================================
Description:  A framework for running large collections of serial or multi-
              threaded applications
Versions:     3.7
License:      GPLv2
Categories:   Core
==============================================================================


Linaro Forge
==============================================================================
Description:  Parallel debugging and profiling tools, DDT and MAP.
Versions:     23.0.3
License:      Not available
Categories:   Programming, profiler, debugger, performance
==============================================================================


Mathematica
==============================================================================
Description:  Mathematical and technical computing package.
Versions:     12.3.1; 13.2.1
License:      http://www.wolfram.com/legal/agreements/wolfram-
              mathematica.html
Categories:   Mathematics, symbolic algebra
==============================================================================


Matlab
==============================================================================
Description:  Matlab programming environment.
Versions:     R2019b; R2021b; R2022b; R2023b
License:      N/A
Categories:   Mathematics, programming, simulation
==============================================================================


Matplotlib
==============================================================================
Description:  Visualization with Python.
Versions:     3.5.3
License:      https://github.com/matplotlib/matplotlib/tree/main/LICENSE
Categories:   Programming, python, visualization, graph, image
==============================================================================


minimap2
==============================================================================
Description:  Minimap2 is a versatile sequence alignment program that aligns
              DNA or mRNA sequences against a large reference database.
              Mappy provides a convenient interface to minimap2.
Versions:     2.14
License:      N/A
Categories:   N/A
==============================================================================


MKL
==============================================================================
Description:  Intel optimized BLAS/LAPACK libraries, also including FFT and
              other mathematical and statistical routines.
Versions:     2018.0.4
License:      https://software.intel.com/en-us/license/intel-simplified-
              software-license
Categories:   Library, Development, Core, BLAS, LAPACK
==============================================================================


mothur
==============================================================================
Description:  This project seeks to develop a single piece of open-source,
              expandable software to fill the bioinformatics needs of the
              microbial ecology community.
Versions:     1.46.1
License:      N/A
Categories:   N/A
==============================================================================


MPI for Python (mpi4py)
==============================================================================
Description:  Numerical libraries for use within Python.
Versions:     3.1.3
License:      https://github.com/mpi4py/mpi4py/blob/master/LICENSE.rst
Categories:   Programming, python, MPI, mpi4py
==============================================================================


MPIFileUtils
==============================================================================
Description:  Parallel file manipulation utilities.
Versions:     0.10.2-arcts
License:      https://github.com/brockpalen/mpifileutils/blob/master/LICENSE
Categories:   Utility
==============================================================================


MPlayer
==============================================================================
Description:  MPlayer is a free and open-source media player software that
              supports a wide variety of audio and video formats. It runs on
              multiple platforms including Linux, Windows, and macOS.
Versions:     1.5
License:      GNU General Public License version 2
Categories:   media player, multimedia
==============================================================================


MRtrix
==============================================================================
Description:  MRtrix provides a set of tools to perform various advanced
              diffusion MRI analyses.
Versions:     3.0.3-dfd3360; 3.0.4
License:      Mozilla 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/pkgs/coe/c/nagf95/6.1-6120/lic_agr.txt
Categories:   fortran, compiler
==============================================================================


Natural Bond Orbital (NBO)
==============================================================================
Description:  Computational chemistry program for the analysis of many-
              electron molecular wavefunctions.
Versions:     7.0
License:      (c) Copyright 1996-2018 Board of Regents of the University of
              Wisconsin System on behalf of the Theoretical Chemistry
              Institute. All rights reserved.
Categories:   Computational Chemistry, Quantum Chemistry, simulation.
==============================================================================


ncftp
==============================================================================
Description:  NcFTP Client is a set of application programs implementing the
              File Transfer Protocol.
Versions:     3.2.6
License:      N/A
Categories:   N/A
==============================================================================


NERS-CLASS-SW
==============================================================================
Description:  [SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu]
              Software for NERS classses: mcc2-3, rebus, dif3d, twodant.
Versions:     1.0
License:      N/A
Categories:   Nuclear
==============================================================================


NetCDF
==============================================================================
Description:  Libraries for creating and manipulating NetCDF files.
Versions:     4.8.1; 4.6.2
License:      https://www.ucar.edu/terms-of-use
Categories:   Library, Development, Core
==============================================================================


NetCDF Fortran
==============================================================================
Description:  Libraries for creating and manipulating NetCDF files using
              Fortran.
Versions:     4.5.3
License:      https://www.ucar.edu/terms-of-use
Categories:   Library, Development, Core
==============================================================================


NetCDF-CXX
==============================================================================
Description:  C++ API to the NetCDF-C libraries.
Versions:     4.3.1
License:      https://www.ucar.edu/terms-of-use
Categories:   Library, Development, Core
==============================================================================


NumPy
==============================================================================
Description:  Numerical libraries for use within Python.
Versions:     1.22.3
License:      https://github.com/numpy/numpy
Categories:   Programming, numerical library, BLAS, LAPACK, python
==============================================================================


openblas
==============================================================================
Description:  BLAS provides standard interfaces for linear algebra,
              including vector-vector operations, matrix-vector operations,
              and matrix-matrix operations.
Versions:     0.3.19; 0.3.23
License:      https://opensource.org/licenses/BSD-3-Clause
Categories:   Programming, C++, library
==============================================================================


OpenJDK
==============================================================================
Description:  OpenJDK is a free and open-source implementation of the Java
              Platform.
Versions:     18.0.1.1
License:      GPLv2 with linking exception
Categories:   Java, programming
==============================================================================


OpenMPI
==============================================================================
Description:  OpenMPI implementation of the MPI protocol
Versions:     4.1.3; 4.1.4; 4.1.6
License:      https://www.open-mpi.org/community/license.php
Categories:   Utility, Development, Core
==============================================================================


openslide
==============================================================================
Description:  OpenSlide reads whole slide image files.
Versions:     3.4.1
License:      N/A
Categories:   N/A
==============================================================================


Pandas
==============================================================================
Description:  Data analysis and manipulation.
Versions:     1.4.2
License:      https://github.com/pandas-dev/pandas
Categories:   Programming, statistics, data analysis, data management,
              python
==============================================================================


Pandoc
==============================================================================
Description:  A universal document converter.
Versions:     2.17.1.1
License:      http://www.gnu.org/copyleft/gpl.html
Categories:   Utility, document converter, markup
==============================================================================


Parabricks
==============================================================================
Description:  Parabricks is a software suite for performing secondary
              analysis of next generation sequencing (NGS) of DNA and RNA
              data
Versions:     4.0.1-1
License:      Apache License 2.0 https://docs.nvidia.com/clara/parabricks/4.
              0.1/documentation/thirdpartysoftwarenotices.html
Categories:   Genomics, Healthcare, big data, pipelines
==============================================================================


Parallel HDF5 (PHDF5)
==============================================================================
Description:  Parallel HDF5 data libraries and utilities.
Versions:     1.12.1
License:      https://www.hdfgroup.org/products/licenses.html
Categories:   Utility, programming, library
==============================================================================


Paraview
==============================================================================
Description:  Paraview data analysis and visualization application.
Versions:     5.12.0
License:      http://www.paraview.org/paraview-license/
Categories:   Visualization, data analysis
==============================================================================


PGI compilers
==============================================================================
Description:  Compiler suite.
Versions:     20.4
License:      http://www.pgroup.com/doc/LICENSE.txt
Categories:   Compiler, development, debugger, profiler
==============================================================================


plink
==============================================================================
Description:  PLINK a whole genome association analysis toolset.
Versions:     1.9; 2.0; 2.3a; 2.3a3; 2.3dev
License:      GPLv3
Categories:   Bioinformatics
==============================================================================


Poetry
==============================================================================
Description:  Python packaging and dependency management.
Versions:     1.6.1
License:      https://github.com/python-poetry/poetry
Categories:   Programming, dependency management, python
==============================================================================


PROJ
==============================================================================
Description:  PROJ is a generic coordinate transformation software.
Versions:     9.0.0; 9.3.1
License:      MIT
Categories:   GIS, Library
==============================================================================


py-macs2
==============================================================================
Description:  MACS2 Model-based Analysis of ChIP-Seq
Versions:     2.2.4
License:      N/A
Categories:   N/A
==============================================================================


py-weblogo
==============================================================================
Description:  WebLogo is a web based application designed to make the
              generation of sequence logos as easy and painless as possible.
Versions:     3.7.12
License:      N/A
Categories:   N/A
==============================================================================


PyArrow
==============================================================================
Description:  In-memory analytics for use within Python.
Versions:     8.0.0
License:      https://github.com/apache/arrow/blob/master/LICENSE.txt
Categories:   Programming, python
==============================================================================


Python
==============================================================================
Description:  Python is a general purpose programming language
Versions:     3.10.4; 3.11.5; 3.9.12
License:      https://docs.python.org/3/license.html
Categories:   Programming, language
==============================================================================


PyTorch
==============================================================================
Description:  Python tensor library for deep learning.
Versions:     1.12.1; 2.0.1
License:      https://pytorch.org/
Categories:   Programming, python, machine learning, tensor, GPU
==============================================================================


R
==============================================================================
Description:  R environment for statistical computing and graphics
Versions:     4.2.0; 4.3.1
License:      GPL, https://www.r-project.org/Licenses/
Categories:   Statistics, graphics, big data, data science
==============================================================================


r-seurat
==============================================================================
Description:  Tools for Single Cell Genomics
Versions:     4.1.1
License:      N/A
Categories:   N/A
==============================================================================


raxml
==============================================================================
Description:  RAxML (Randomized Axelerated Maximum Likelihood) is a program
              for sequential and parallel Maximum Likelihood based inference
              of large phylogenetic trees.
Versions:     8.2.11; 8.2.12
License:      N/A
Categories:   N/A
==============================================================================


rclone
==============================================================================
Description:  rclone is a command line program to sync files and directories
              to and from many cloud storage providers
Versions:     1.57.0
License:      MIT License
Categories:   File transfer, Utilities
==============================================================================


Rgeospatial
==============================================================================
Description:  A collection of R geospatial libraries
Versions:     2022-08-18; 2023-04-25; 2023-07-01
License:      GPL, https://www.r-project.org/Licenses/
Categories:   Statistics, graphics, big data, data science, geospatial,
              geography, spatial, map
==============================================================================


rmats
==============================================================================
Description:  MATS is a computational tool to detect differential
              alternative splicing events from RNA-Seq data.
Versions:     4.0.2
License:      N/A
Categories:   N/A
==============================================================================


Ropenblas
==============================================================================
Description:  R OpenBLAS provides an optimized library for faster linear
              algebra computations.
Versions:     4.2.0; 4.3.1
License:      GPL, https://www.r-project.org/Licenses/
Categories:   Statistics, linear algebra, big data, data science
==============================================================================


RStudio Server
==============================================================================
Description:  RStudio Desktop is a graphichal user interface for R.
Versions:     2022.07.1; 2022.07.2; 2023.06.1
License:      AGPL v3
Categories:   Statistics, graphics, big data, data science, IDE
==============================================================================


Rtidyverse
==============================================================================
Description:  R Tidyverse environment for statistical computing and graphics
Versions:     4.2.0; 4.3.1
License:      GPL, https://www.r-project.org/Licenses/
Categories:   Statistics, graphics, big data, data science, tidyverse
==============================================================================


salmon
==============================================================================
Description:  Salmon is a tool for quantifying the expression of transcripts
              using RNA-seq data.
Versions:     1.9.0
License:      N/A
Categories:   N/A
==============================================================================


samtools
==============================================================================
Description:  SAM Tools provide various utilities for manipulating
              alignments in the SAM format, including sorting, merging,
              indexing and generating alignments in a per-position format
Versions:     1.13; 1.9
License:      N/A
Categories:   N/A
==============================================================================


SAS
==============================================================================
Description:  SAS statistical system software.
Versions:     9.4-TS1M7
License:      Not available
Categories:   Statistics, econometrics
==============================================================================


SciPy
==============================================================================
Description:  Scientific libraries for use within Python.
Versions:     1.8.0
License:      https://github.com/scipy/scipy
Categories:   Programming, python, solver
==============================================================================


seqkit
==============================================================================
Description:  A cross-platform and ultrafast toolkit for FASTA/Q file
              manipulation in Golang.
Versions:     2.3.0
License:      N/A
Categories:   N/A
==============================================================================


ShellCheck
==============================================================================
Description:  ShellCheck, a static analysis tool for shell scripts
Versions:     0.9.0
License:      GPLv3
              https://github.com/koalaman/shellcheck/blob/master/LICENSE
Categories:   Shell, Bash, Linter, static-analysis, developer-tools
==============================================================================


Singularity
==============================================================================
Description:  Program for running containerized applications
Versions:     3.10.4; 3.11.1
License:      https://github.com/sylabs/singularity/blob/master/LICENSE.md
Categories:   Container, docker, reproducible research
==============================================================================


spaceranger
==============================================================================
Description:  a set of analysis pipelines that process Visium spatial RNA-
              seq output and brightfield microscope images
Versions:     2.0.1; 2.1.1; 3.0.0
License:      GPLv2
Categories:   Bioinformatics
==============================================================================


Spack Package Manager
==============================================================================
Description:  A flexible package manager supporting multiple versions,
              configurations, platforms, and compilers.
Versions:     0.21
License:      Apache-2.0
Categories:   Software Installation, compiling, package manager
==============================================================================


spades
==============================================================================
Description:  SPAdes - St. Petersburg genome assembler - is intended for
              both standard isolates and single-cell MDA bacteria
              assemblies.
Versions:     3.15.5
License:      N/A
Categories:   N/A
==============================================================================


sratoolkit
==============================================================================
Description:  The NCBI SRA Toolkit enables reading ('dumping') of sequencing
              files from the SRA database and writing ('loading') files into
              the .sra format.
Versions:     2.10.9; 2.9.6
License:      N/A
Categories:   N/A
==============================================================================


star
==============================================================================
Description:  STAR is an ultrafast universal RNA-seq aligner.
Versions:     2.7.11a; 2.7.6a
License:      N/A
Categories:   N/A
==============================================================================


Star-CCM+
==============================================================================
Description:  Star-CCM+ is a CFD application that supports parallel
              processing.
Versions:     17.04.007-R8; 17.04.007
License:      Academic Research
Categories:   CFD
==============================================================================


Stata/MP
==============================================================================
Description:  Statistical analysis software.
Versions:     17; 18
License:      http://www.stata.com/order/end-user-license-agreement/
Categories:   Statistics, econometrics
==============================================================================


Stata/SE
==============================================================================
Description:  Statistical analysis software.
Versions:     17; 18
License:      http://www.stata.com/order/end-user-license-agreement/
Categories:   Statistics, econometrics
==============================================================================


stringtie
==============================================================================
Description:  Transcript assembly and quantification for RNA-Seq
Versions:     2.2.1; 2.1.7
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
==============================================================================


TBB
==============================================================================
Description:  Intel Thread Building Blocks.
Versions:     2022.1.2
License:      https://software.intel.com/en-us/articles/end-user-license-
              agreement
Categories:   Library, development, core, thread
==============================================================================


Tecplot 360 & Tecplot Chorus
==============================================================================
Description:  Plotting and visualization software that gives full control
              over 2-D and 3-D plot parameters.
Versions:     2022r1
License:      N/A
Categories:   plotting, visualization
==============================================================================


TensorFlow
==============================================================================
Description:  Machine learning platform for use within Python.
Versions:     2.7.0
License:      Apache License 2.0
Categories:   Programming, machine learning library, python
==============================================================================


TensorRT
==============================================================================
Description:  An SDK for high-performance deep learning inference.
Versions:     11.8-v8.6.1
License:      Apache License 2.0
Categories:   Programming, Machine Learning, Tensorflow, Inference
==============================================================================


tmux
==============================================================================
Description:  Terminal multiplexer
Versions:     3.3a
License:      https://opensource.org/licenses/ISC
Categories:   Terminal, multiplex
==============================================================================


trimgalore
==============================================================================
Description:  Trim Galore! is a wrapper around Cutadapt and FastQC to
              consistently apply adapter and quality trimming to FastQ
              files, with extra functionality for RRBS data.
Versions:     0.6.7
License:      N/A
Categories:   N/A
==============================================================================


Trinity
==============================================================================
Description:  Trinity assembles transcript sequences from Illumina RNA-Seq
              data.
Versions:     2.15.1
License:
              https://raw.githubusercontent.com/trinityrnaseq/trinityrnaseq/
              master/LICENSE
Categories:   Bioinformatics, Assembly, Transcriptome
==============================================================================


UCX
==============================================================================
Description:  Unified Communication X (UCX)
Versions:     1.14.1
License:      https://github.com/openucx/ucx?tab=License-1-ov-file#readme
Categories:   Communication
==============================================================================


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


valgrind
==============================================================================
Description:  An instrumentation framework for building dynamic analysis.
Versions:     3.20.0
License:      N/A
Categories:   N/A
==============================================================================


VASP
==============================================================================
Description:  [SPECIAL LICENSE REQUIRED: contact arc-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:     2.15.05; 1.3.0
License:      https://www.nasm.us/
Categories:   assembler, programming
==============================================================================