Modules specific to Niagara
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NiaEnv/2019b
| Module | Version(s) | Documentation | Description |
|---|---|---|---|
| CCEnv | Using modules | Alliance (formerly Compute Canada) software modules. Must be loaded to see Alliance (formerly Compute Canada) modules in 'module spider'.
| |
| antlr | 2.7.7 | ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions
| |
| ants | 2.3.1 | ANTs extracts information from complex datasets that include imaging
| |
| arm-forge | 21.0.3 | Arm Forge is the complete toolsuite for software development - with everything needed to debug, profile, optimize, edit and build C, C++ and Fortran applications on Linux for high performance - from single threads through to complex parallel HPC codes with MPI, OpenMP, threads or CUDA.
| |
| armadillo | 9.700.2 | Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use
| |
| arpack-ng | 3.7.0 | ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems
| |
| autodiff | 0.5.11 | ||
| autotools | 2018b 2018 | The standard GNU build tools: autoconf, automake and libtool
| |
| bcftools | 1.8 1.12(E) 1.13(E) | SAMtools is a suite of programs for interacting with high-throughput sequencing data
| |
| bedtools | 2.29.0 2.30.0 | The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage
| |
| blast+ | 2.9.0 | Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences
| |
| blitz++ | 1.0.1 | Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in C++ with a speed comparable to Fortran implementations, while preserving an object-oriented interface
| |
| boost | 1.69.0 1.70.0 1.73.0 1.78.0 | Boost provides free peer-reviewed portable C++ source libraries
| |
| boost-python | 1.69.0 1.70.0 1.75.0 | Boost provides free peer-reviewed portable C++ source libraries, including boost:python
| |
| bowtie2 | 2.3.4.3 2.4.4 | Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences
| |
| bwa | 0.7.17 | Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome
| |
| bwa-mem2 | 2.0 | Bwa-mem2 is the next version of the bwa-mem algorithm in bwa
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| cairo | 1.17.2 | Cairo is a 2D graphics library with support for multiple output devices
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| cairo | 1.17.2 | Cairo is a 2D graphics library with support for multiple output devices
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| cereal | 1.2.2 | A C++11 library for serialization
| |
| cfitsio | 3.450 | CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format
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| cgal | 5.1 | ||
| cget | 0.1.9 | Cmake package retrieval
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| chaiscript | 6.1.0 | Embedded Scripting Language Designed for C++
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| cmake | 3.13.4 3.14.5 3.17.3 3.21.4 | CMake, the cross-platform, open-source build system
| |
| cp2k | 6.1 | CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems
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| cufflinks | 2.2.1 | Cufflinks Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples
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| cufflinks | 2.2.1 | Cufflinks Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples
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| cutadapt | 2.10 | ||
| ddd | 3.3.12 | GNU DDD is a graphical front-end for command-line debuggers such as GDB, DBX, WDB, Ladebug, JDB, XDB, the Perl debugger, the bash debugger bashdb, the GNU Make debugger remake, or the Python debugger pydb
| |
| arm-forge | 22.0.2 | Arm Forge | DDT debugger and MAP profiler
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| dealii | 9.2.0 | deal
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| doxygen | 1.8.17 | Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D
| |
| eigen | 3.3.7 | Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms
| |
| elpa | 2017.05.003 2020.05.001 | Eigenvalue SoLvers for Petaflop-Applications
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| expect | 5.45.4 | Expect is a tool for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc.
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| fastqc | 0.11.9 | ||
| fenics | 2019.1.0 | FEniCS is a computing platform for solving partial differential equations
| |
| ffmpeg | 3.4.2 | A complete, cross-platform solution to record, convert and stream audio and video
| |
| fftw | 3.3.8 | FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data
| |
| fmt | 4.1.0 | fmt (formerly cppformat) is an open-source formatting library
| |
| freesurfer | 6.0.0 7.1.0 | FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data
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| fsl | 6.0.4 | ||
| gatk | 4.1.7.0 | ||
| gcc | 8.3.0 9.2.0 9.4.0 | Niagara Quickstart | The GNU Compiler Collection C, C++, and Fortran
|
| gdal | 2.4.1 | GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation
| |
| geos | 3.7.1 | GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)
| |
| git | 2.21.0 2.30.1 | Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency
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| git-annex | 2.8.1 8.20200618 | git-annex allows managing files with git, without checking the file contents into git
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| git-lfs | 2.13.2 | Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub
| |
| glib | 2.48.2 | ||
| gmp | 6.1.2 6.2.0 | GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers
| |
| gmt | 6.0.0 | Generic Mapping Tools is an open source collection of many command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc
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| gnu-parallel | 20190322 20191122 | Running Serial Jobs on Niagara | GNU parallel is a shell tool for executing (usually serial) jobs in parallel
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| gnuplot | 5.2.7 | Portable interactive, function plotting utility
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| go | 1.13 | Go is an open source programming language that makes it easy to build simple, reliable, and efficient software
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| googletest | 1.10.0 | Google's C++ test framework
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| gperf | 3.1 | GNU gperf is a perfect hash function generator
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| graphviz | 2.40.1 | Graphviz is open source graph visualization software
| |
| gromacs | 2018.6-plumed-2.5.1 2018.6 | GROMACS | GROMACS is a versatile package to perform molecular dynamics, i
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| gromacs-ls | 2016.3 | GROMACS-LS is a custom version of GROMACS developed for local stress calculations from molecular simulations.
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| gsl | 2.5 2.7 | The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers
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| hdf5 | 1.8.21 1.10.5 1.10.7 | HDF5 | HDF5 is a data model, library, and file format for storing and managing data
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| hh-suite | 3.3.0 | The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs)
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| highfive | 2.3 | HighFive is a modern header-only C++11 friendly interface for libhdf5.
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| htslib | 1.12(E) 1.13(E) | ||
| icu | 68.1 | International Components for Unicode
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| imagemagick | 6 | ||
| intel | 2019u3 2019u4 2019u5 2020u2 2020u4 | Niagara Quickstart | Intel compilers suite for C, C++, and Fortran, including the MKL, TBB, IPP, DAAL, and PSTL libraries
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| intelmpi | 2019u3 2019u4 2019u5 2020u2 2020u4 | Niagara Quickstart | |
| intelpython2 | 2019u3 2019u4 2019u5 | Python | Intel Python distribution for python 2, based on anaconda
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| intelpython3 | 2019u3 2019u4 2019u5 | Python | Intel Python distribution for python 3, based on anaconda
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| inteltools | 2019u4 | ||
| itk | 4.13.2 | Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data
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| jags | 4.3.0 | JAGS is Just Another Gibbs Sampler
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| java | 1.8.0_201 | Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers
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| jellyfish | 2.3.0 | Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA
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| julia | 1.1.0 1.5.3 1.6.1 1.7.2 | A high-level, high-performance dynamic language for technical computing
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| julia | 1.1.0 1.5.3 1.6.1 1.7.2 | A high-level, high-performance dynamic language for technical computing
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| lammps | 20Nov2019 29Mar2019 | The 'Large-scale Atomic/Molecular Massively Parallel Simulator' is a classical molecular dynamics simulation
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| libgit2 | 1.1.0 | ||
| libint | 1.1.5 2.6-shared 2.6.0 | Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory
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| libsodium | 1.0.18 | Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more
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| libxc | 4.0.5 4.3.4 5.0.0 | Libxc is a library of exchange-correlation functionals for density-functional theory
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| libxslt | 1.1.34 | Libxslt is the XSLT C library developed for the GNOME project
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| lmdb | 0.9.23 | OpenLDAP's Lightning Memory-Mapped Database (LMDB) library
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| lsb-release | versionless | ||
| mcr | R2019a | MATLAB | The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed
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| mercurial | 5.1 | Mercurial is a free, distributed source control management tool
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| meson | 0.51.2 | Meson is a cross-platform build system designed to be both as fast and as user friendly as possible
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| metis | 5.1.0-shared 5.1.0 | METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices
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| mii | 1.1.1 | A smart search engine for module environments.
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| mkl | 2019u3 2019u4 | Niagara Quickstart | Intel Math Kernel Library
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| mothur | 1.42.3 | Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community
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| mpfr | 4.0.2 4.1.0 | The MPFR library is a C library for multiple-precision floating-point computations with correct rounding
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| mrbayes | 3.2.7 | MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models
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| mrtrix | 3.0.0 | ||
| mumps | 5.1.2 5.2.1 | A parallel sparse direct solver
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| muscle | 3.8.31 | MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW
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| namd | 2.14 | NAMD | NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems
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| ncl | 6.6.2 | NCL is an interpreted language designed specifically for scientific data analysis and visualization
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| nco | 4.8.1 | Python bindings for NCO
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| ncview | 2.1.7 | Ncview is a visual browser for netCDF format files
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| netcdf | 4.6.3 | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data
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| ninja | 1.9.0 | Ninja is a small build system with a focus on speed
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| numdiff | 5.9.0 | numdiff can be used to compare putatively similar files line by line and field by field, ignoring small numeric differences or/and different numeric formats
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| octave | 5.2.0 | Octave | GNU Octave is a high-level interpreted language, primarily intended for numerical computations
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| openblas | 0.3.7 | OpenBLAS is an optimized BLAS library based on GotoBLAS2 1
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| opencv | 4.5.0 | OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library
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| openfoam | 7-broken 19.06 20.06 20.12 | ||
| openjpeg | 2.3.1 | OpenJPEG is an open-source JPEG 2000 codec, developed in order to promote the use of JPEG 2000, a still-image compression standard from the Joint Photographic Experts Group (JPEG)
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| openmpi | 3.1.3 4.0.1 4.0.3 4.1.1 | Niagara Quickstart | The Open MPI Project is an open source MPI-2 implementation
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| orthofinder | 2.3.3 | Program for identifying orthologous protein sequence families
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| osu-micro-benchmarks | 5.6.1 5.7.1 | OSU Micro-Benchmarks
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| pandoc | 2.7.3 | If you need to convert files from one markup format into another, pandoc is your swiss-army knife
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| papi | 6.0.0.1 | Performace Application Programming Interface
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| paraview-offscreen | 5.9.1 | Visualization | Off-screen rendering with ParaView, a scientific parallel visualizer
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| parmetis | 4.0.3 | ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices
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| pcre2 | 10.35 | A set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5
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| perl | 5.28.1 5.30.3 5.34.0 | Larry Wall's Practical Extraction and Report Language
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| petsc | 3.9.3 3.10.5 3.11.3 3.13.5 | PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations
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| pgplot | 5.2.2 | Graphics subroutine library for C/C++ and Fortran
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| pixman | 0.38.4 | The Pixman library is a C library, part of the Cairo package, used for 2D graphics
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| plink | 1.90b6 | PLINK is a whole-genome association analysis toolset, version 1
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| plink2 | 2.00a3 | PLINK is a whole-genome association analysis toolset, version 2
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| plumed | 2.5.1 | PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines
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| pnetcdf | 1.11.0 1.11.2 | Parallel netCDF: A Parallel I/O Library for NetCDF File Access
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| postgresql | 14.1 | PostgreSQL is a powerful, open source object-relational database system with over 30 years of active development that has earned it a strong reputation for reliability, feature robustness, and performance.
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| proj | 4.9.3 6.0.0 | Cartographic projections and coordinate transformations library
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| python | 2.7.15 3.6.8 3.7.9 3.8.5 3.9.8 | Python | Python is a programming language that lets you work more quickly and integrate your systems more effectively
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| qbatch | 2.1.4 2.1.5 2.2.1 2.3.0 | qbatch is a tool for executing commands in parallel across a compute cluster
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| qhull | 2020.2 | Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram
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| qt | 4.8.7 5.12.4 | Qt is a comprehensive cross-platform C++ application framework
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| quantum-espresso | 6.4.1 6.5-perturbo 6.5-w90-perturbo | An integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale
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| r | 3.5.3 3.6.1 3.6.3 4.0.3 4.1.2 | R is a free software environment for statistical computing and graphics
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| r | 3.5.3 3.6.1 3.6.3 4.0.3 4.1.2 | R is a free software environment for statistical computing and graphics
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| rarray | 1.2 2.0.0 2.1.1 2.3.0 | Library for runtime multi-dimensional arrays in C++
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| rosetta | 3.13 | Rosetta is the premier software suite for modeling macromolecular structures
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| rsync | 3.1.3 | Data Management | Fast, versatile, remote file-copying tool
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| rust | 1.47.0 | Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety
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| salmon | 0.14.2 0.99.0-beta2 | ||
| sambamba | 0.7.1 | ||
| samtools | 1.9 1.11 1.12 1.13 | SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format
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| scalapack | 2.0.2 | The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers
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| scons | 3.0.5 | SCons is a software construction tool
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| scotch | 6.0.6 | Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning
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| shengbte | 1.1.1 | Software package for solving the Boltzmann Transport Equation for phonons
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| siesta | master-27Oct2019 4.0.2 4.1-b4-transiesta-netcdf4 4.1-b4-transiesta 4.1-b4 4.1.5-util 4.1.5 | Computer implementation of the SIESTA method to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids
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| singularity | 3.8.0 | Singularity | Singularity is a portable application stack packaging and runtime utility
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| sox | 14.4.2 | SoX, the Swiss Army knife of sound processing programs.
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| spglib | 1.10.3 | Spglib is a C library for finding and handling crystal symmetries
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| sqlite | 3.23.0 | SQLite: SQL Database Engine in a C Library
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| stacks | 2.55 | Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform
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| subversion | 1.10.4 | Subversion is an open source version control system
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| suitesparse | 5.8.1 | SuiteSparse is a suite of sparse matrix software
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| sundials | 5.3.0 | SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers
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| superlu | 5.2.1 | SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines
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| swig | 3.0.12 4.0.1 | SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages
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| tbb | 2019u8 2019u9 | Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable, composable and have future-proof scalability
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| texlive | 2019 | High-quality typesetting programs TeX and LaTeX
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| thirdorder | 1.1.1 | Set of scripts to help users of ShengBTE and almaBTE create FORCE_CONSTANTS_3RD files in an efficient and convenient manner
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| tmux | 3.2a | tmux is a terminal multiplexer: it enables a number of terminals to be created, accessed, and controlled from a single screen. tmux may be detached from a screen and continue running in the background, then later reattached.
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| trilinos | 12.12.1 | The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems
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| trimgalore | 0.6.5 | ||
| trinityrnaseq | 2.8.1 | Trinity RNA-Seq de novo transcriptome assembly
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| udunits | 2.2.26 | UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement
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| valgrind | 3.14.0 | Introduction To Performance | Valgrind-3
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| vcftools | 0.1.16 | A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project
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| visit | 3.2.1 3.2.2 | Visualization | Open Source, interactive, scalable, visualization, animation and analysis tool.
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| vmd | 1.9.4a38 | Visualization | VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting
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| vsearch | 2.14.2 | VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting
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| vtk | 8.1.0 8.2.0 9.0.1 | The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization
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| zlib | 1.2.11 | zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system
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| zlib | 1.2.11 | zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system
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NiaEnv/2018a
| Module | Version(s) | Documentation | Description |
|---|---|---|---|
| CCEnv | Using modules | Alliance (formerly Compute Canada) software modules. Must be loaded to see Alliance (formerly Compute Canada) modules in 'module spider'.
| |
| anaconda2 | 5.1.0 | Python | Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture
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| anaconda3 | 5.1.0 5.2.0 2018.12 | Python | Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture
|
| antlr | 2.7.7 | ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions
| |
| ants | 2.3.1 | ANTs extracts information from complex datasets that include imaging
| |
| armadillo | 8.500.1 | Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use
| |
| arpack-ng | 3.5.0 | ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems
| |
| aspect | 2.0.0 2.0.1 2.1.0-pre 2.1.0 | Finite element parallel code to simulate problems in thermal convection in both 2D and 3D models
| |
| aspera-client | 3.8.1 | Command-line interface for Aspera, a data transport and streaming technology
| |
| autotools | 2017 | The standard GNU build tools: autoconf, automake and libtool
| |
| bayestraits | 3.0.1 | BayesTraits is a computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available
| |
| bazel | 0.11.1 0.15.0 | Bazel is a build tool that builds code quickly and reliably
| |
| bedops | 2.4.35 | 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
| |
| bedtools | 2.27.1 | The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage
| |
| blast+ | 2.7.1 | Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences
| |
| boost | 1.63.0 1.66.0 1.67.0 | Boost provides free peer-reviewed portable C++ source libraries
| |
| boost-mpi | 1.67.0 | Boost provides free peer-reviewed portable C++ source libraries
| |
| bwa | 0.7.17 | Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome
| |
| cdo | 1.9.4 | CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data
| |
| cereal | 1.2.2 | A C++11 library for serialization
| |
| cfitsio | 3.430 | CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format
| |
| chaiscript | 6.1.0 | Embedded Scripting Language Designed for C++
| |
| cmake | 3.10.3 3.11.0 3.11.1 | CMake, the cross-platform, open-source build system
| |
| cp2k | 6.1 | CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems
| |
| dakota-mpi | 6.7.0 | The Dakota project delivers both state-of-the-art research and robust, usable software for optimization and Unicertainly Quantification
| |
| dcm2niix | 1.0.20200331 | dcm2niix is a designed to convert neuroimaging data from the DICOM format to the NIfTI format
| |
| arm-forge | 22.0.2 | Arm Forge | DDT debugger and MAP profiler
|
| diamond | 0.9.23 | Accelerated BLAST compatible local sequence aligner
| |
| eigen | 3.3.4 | Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms
| |
| elpa | 2016.05.003 2017.05.003 2018.05.001 | Eigenvalue SoLvers for Petaflop-Applications
| |
| esmf | 7.1.0r | The Earth System Modeling Framework (ESMF) is software for building and coupling weather, climate, and related models
| |
| fastme | 2.1.6.1 | FastME: a comprehensive, accurate and fast distance-based phylogeny inference program
| |
| fenics | 2017.2.0 2018.1.0 | FEniCS is a computing platform for solving partial differential equations
| |
| fetk | 1.5 | The Finite Element ToolKit is a collaboratively developed, evolving collection of adaptive finite element method software libraries and tools for solving coupled systems of nonlinear geometric partial differential equations
| |
| ffmpeg | 3.4.2 | A complete, cross-platform solution to record, convert and stream audio and video
| |
| fftw | 3.3.7 | FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data
| |
| fftw-mpi | 3.3.7 | FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data
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| fmt | 3.0.2 4.1.0 | fmt (formerly cppformat) is an open-source formatting library
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| foam-extend | 4.0 | The foam-extend project is a fork of the OpenFOAM open source library for Computational Fluid Dynamics
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| freesurfer | 5.3.0 6.0.0 | FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data
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| g_mmpbsa | 5.1.2 | Molecular mechanics/Poisson-Bolzmann surface area method for GROMACS
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| gamess | 14Feb2018 | GAMESS | General Atomic and Molecular Electronic Structure System is a general ab initio quantum chemistry package
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| gc | 7.6.6 | The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new
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| gcc | 4.9.4 7.3.0 | Niagara Quickstart | The GNU Compiler Collection C, C++, and Fortran
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| gdb | 8.1 | Performance And Debugging Tools: Niagara | The GNU Project Debugger
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| git | 2.16.3 | Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency
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| git-annex | 2.8.1 8.20200618 | git-annex allows managing files with git, without checking the file contents into git
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| git-lfs | 2.13.2 | Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub
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| glib | 2.22.5 | GLib is one of the base libraries of the GTK+ project
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| gmp | 6.1.2 | GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers
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| gnu-parallel | 20180322 | Running Serial Jobs on Niagara | GNU parallel is a shell tool for executing (usually serial) jobs in parallel
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| gnuplot | 5.2.2 | Portable interactive, function plotting utility
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| go | 1.13 | Go is an open source programming language that makes it easy to build simple, reliable, and efficient software
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| googletest | 1.8.0 | Google's C++ test framework
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| gromacs | 5.1.4 2016.5-plumed-2.4.1 2016.5 2019.1 | GROMACS | GROMACS is a versatile package to perform molecular dynamics, i
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| gsl | 2.4 | The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers
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| guile | 2.2.3 | Guile is a programming language, designed to help programmers create flexible applications that can be extended by users or other programmers with plug-ins, modules, or scripts
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| harminv | 1.4.1 | Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids
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| harminv | 1.4.1 | Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids
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| hdf5 | 1.8.20 1.10.2 | HDF5 | HDF5 is a data model, library, and file format for storing and managing data
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| hdf5-mpi | 1.8.20 1.10.2 | HDF5 | HDF5 is a data model, library, and file format for storing and managing data
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| hisat2 | 2.1.0 | HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome)
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| hpn-ssh | 7.7p1-14v15 | Optimized ssh protocol
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| htseq | 0.11.1 | A framework to process and analyze data from high-throughput sequencing (HTS) assays
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| imake | 1.0.7 | imake is a Makefile-generator that is intended to make it easier to develop software portably for multiple systems
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| intel | 2017.7 2018.1 2018.2 2018.3 | Niagara Quickstart | Intel compilers suite for C, C++, and Fortran, including the MKL, TBB, IPP, DAAL, and PSTL libraries
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| intel-mpi-benchmarks | 2018.1 | a set of elementary benchmarks that conform to MPI-1, MPI-2, and MPI-3 standard
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| intelmpi | 2017.7 2018.1 2018.2 2018.3 | Niagara Quickstart | Intel MPI library with compiler wrappers for C, C++, and Fortran
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| intelpython2 | 2018.2 | Python | Intel Python distribution for python 2, based on anaconda
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| intelpython3 | 2018.2 | Python | Intel Python distribution for python 3, based on anaconda
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| itk | 4.13.0 | Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data
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| jasper | 2.0.14 | The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard
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| java | 1.8.0_162 | Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers
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| julia | 1.0.0 1.1.0 | A high-level, high-performance dynamic language for technical computing
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| julia | 1.0.0 1.1.0 | A high-level, high-performance dynamic language for technical computing
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| lammps | 11May2018 22Sep2017 | The 'Large-scale Atomic/Molecular Massively Parallel Simulator' is a classical molecular dynamics simulation
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| libatomic_ops | 7.6.4 | C/C++ Library for semi-portable access to hardware-provided atomic memory update operations on a number of architectures
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| libconfig | 1.7.2 | Libconfig is a simple library for processing structured configuration files
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| libctl | 4.0.1 4.1.2 | libctl is a free Guile-based library implementing flexible control files for scientific simulations
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| libevent | 2.1.8 | The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached
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| libffi | 3.2.1 | The libffi library provides a portable, high level programming interface to various calling conventions
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| libint | 1.1.5 1.1.6 | Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory
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| libsodium | 1.0.18 | Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more
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| libtiff | 4.0.9 | tiff: Library and tools for reading and writing TIFF data files
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| libunistring | 0.9.9 | This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard
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| libxc | 3.0.0 4.0.3 4.0.5 | Libxc is a library of exchange-correlation functionals for density-functional theory
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| libxslt | 1.1.32 | Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform)
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| libxsmm | 1.9 | LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86)
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| libyaml | 0.1.7 | LibYAML is a YAML 1
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| lmdb | 0.9.22 | OpenLDAP's Lightning Memory-Mapped Database (LMDB) library
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| lsb-release | versionless | ||
| makedepend | 1.0.5 | The makedepend package contains a C-preprocessor like utility to determine build-time dependencies
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| mcl | 14-137 | The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs
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| mcr | R2018a | MATLAB | The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed
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| meep | 1.4.3 1.5.0 | Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems
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| meep-mpi | 1.4.3 1.5.0 | Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems
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| mercurial | 4.6 | Mercurial is a free, distributed source control management tool
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| metis | 5.1.0 | METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices
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| mkl | 2017.7 2018.1 2018.2 2018.3 | Niagara Quickstart | Intel Math Kernel Library
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| mmseqs2 | 7-4e23d | MMseqs2: ultra fast and sensitive search and clustering suite
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| mosh | 1.3.2 | Remote terminal application that allows roaming, supports intermittent connectivity, and provides intelligent local echo and line editing of user keystrokes
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| mpb | 1.6.2 | MIT Photonic-Bands: computation of photonic band structures in periodic media
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| mpb-mpi | 1.6.2 | MIT Photonic-Bands: computation of photonic band structures in periodic media
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| mpfr | 4.0.1 | The MPFR library is a C library for multiple-precision floating-point computations with correct rounding
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| mrtrix | 3.0.0 | ||
| mumps | 5.1.2 | A parallel sparse direct solver
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| mysql | 8.0.13 | MySQL is (as of March 2014) the world's second most widely used open-source relational database management system (RDBMS)
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| namd | 2.13 | NAMD | NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems
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| ncl | 6.4.0 | NCL is an interpreted language designed specifically for scientific data analysis and visualization
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| nco | 4.7.4 4.7.6 | Python bindings for NCO
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| ncview | 2.1.7 | Ncview is a visual browser for netCDF format files
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| netcdf | 4.6.1 | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data
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| netcdf-mpi | 4.6.1 | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data
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| neuron | 7.6.2 | Empirically-based simulations of neurons and networks of neurons
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| octave | 4.4.0 | Octave | GNU Octave is a high-level interpreted language, primarily intended for numerical computations
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| openblas | 0.2.20 | OpenBLAS is an optimized BLAS library based on GotoBLAS2 1
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| opencv | 2.4.13.6 4.1.0 | OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library
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| openfoam | 4.1 5.0-debug 5.0 6 17.12 18.06 18.12 | OpenFOAM is a free, open source CFD software package
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| openmpi | 1.10.7 2.1.3 2.1.4 3.0.1 3.0.2 3.1.0rc3 3.1.0rc4 3.1.0 3.1.1 | Niagara Quickstart | The Open MPI Project is an open source MPI-2 implementation
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| orthofinder | 2.2.7 | Program for identifying orthologous protein sequence families
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| osu-micro-benchmarks | 5.4.3 | OSU Micro-Benchmarks
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| pandoc | 2.7.3 | If you need to convert files from one markup format into another, pandoc is your swiss-army knife
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| paraview | 5.5.0 | Visualization | ParaView is a scientific parallel visualizer
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| paraview-offscreen | 5.6.0 | Visualization | Off-screen rendering with ParaView, a scientific parallel visualizer
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| parmetis | 4.0.3 | ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices
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| patchelf | 0.10 | ||
| perf-reports | 18.2 | ARM performance reports
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| perl | 5.20.3 5.26.1 | Larry Wall's Practical Extraction and Report Language
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| petsc | 3.8.4-debug 3.8.4 3.9.2 | PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations
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| pgplot | 5.2.2-x 5.2.2 | Graphics subroutine library for C/C++ and Fortran
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| pism | 1.0 | Parallel Ice Sheet Model is open source and capable of high resolution
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| plink | 1.07 1.90b6 | ||
| plumed | 2.4.1 | PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines
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| pnetcdf | 1.9.0 | Parallel netCDF: A Parallel I/O Library for NetCDF File Access
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| protobuf | 3.6.1 | Google Protocol Buffers
| |
| python | 2.7.14-anaconda5.1.0 2.7.14 2.7.15 3.6.4-anaconda5.1.0 3.6.5 | Python | Python is a programming language that lets you work more quickly and integrate your systems more effectively
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| qbatch | 2.1 2.1.4 2.1.5 | qbatch is a tool for executing commands in parallel across a compute cluster
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| qhull | 2015.2 | Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram
| |
| qt | 5.11.1 | Qt is a comprehensive cross-platform C++ application framework
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| quantum-espresso | 6.2.1 6.3 | An integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale
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| r | 3.4.3-anaconda5.1.0 3.5.0 3.5.1 | Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture
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| rarray | 1.2 2.1.1 | Library for runtime multi-dimensional arrays in C++
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| rsync | 3.1.3 | Data Management | Fast, versatile, remote file-copying tool
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| rtk | 1.4.0 | An open-source and cross-platform software for fast circular cone-beam CT reconstruction based on the Insight Toolkit
| |
| rust | 1.26.1 1.28.0 | Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety
| |
| samtools | 1.8 | SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format
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| scalapack | 2.0.2 | The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers
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| scons | 3.0.1 | SCons is a software construction tool
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| scotch | 6.0.6 | Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning
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| shengbte | 1.1.1 | Software package for solving the Boltzmann Transport Equation for phonons
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| silo | 4.10.2-bsd | Silo is a library for reading and writing a wide variety of scientific data to binary, disk files
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| singularity | 3.5.3 | Singularity | Singularity is a portable application stack packaging and runtime utility
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| spades | 3.13.0 | Genome assembler for single-cell and isolates data sets
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| spglib | 1.10.3 | Spglib is a C library for finding and handling crystal symmetries
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| sqlite | 3.23.0 | SQLite: SQL Database Engine in a C Library
| |
| stacks | 2.2 | Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform
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| star | 2.6.1b | STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays
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| stringtie | 1.3.5 | StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts
| |
| su2 | 5.0.0 6.0.0 6.1.0 | An open-source collection of software tools written in C++ for performing Partial Differential Equation (PDE) analysis and solving PDE-constrained optimization problems
| |
| subversion | 1.9.7 | Subversion is an open source version control system
| |
| sundials | 2.6.0 2.7.0 3.1.0 | SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers
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| sundials-mpi | 3.1.0 | SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers
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| swig | 3.0.12 | SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages
| |
| texlive | 2019 | High-quality typesetting programs TeX and LaTeX
| |
| thirdorder | 1.1.1 | Set of scripts to help users of ShengBTE and almaBTE create FORCE_CONSTANTS_3RD files in an efficient and convenient manner
| |
| trilinos | 12.12.1 | The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems
| |
| trinityrnaseq | 2.8.1 | Trinity RNA-Seq de novo transcriptome assembly
| |
| udunits | 2.2.26 | UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement
| |
| valgrind | 3.13.0 3.14.0 | Introduction To Performance | Valgrind provides debugging and profiling tools
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| visit | 2.13.1 | Visualization | An open-source, interactive, scalable, visualization, animation and analysis tool
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| vmd | 1.9.4a12 1.9.4a38 | Visualization | VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting
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| vtk | 8.1.1 | The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization
| |
| wrf | 3.9.1.1 |