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[[FurtherTopics/FurtherTopics #Modules| Back to Further Topics]]
 
[[FurtherTopics/FurtherTopics #Modules| Back to Further Topics]]
 
==Applications==
 
==Applications==
−
This is a list of all applications installed on Viper. If you are looking for an application that requires a special license visit: [[Applications/Special Licenses| Applications requiring special licenses]].
+
The following is a list of core applications installed on Viper, with links to further information on using those applications on Viper. If you are looking for an application that requires a special license visit: [[Applications/Special Licenses| Applications requiring special licenses]].
  
 
If you are looking for how to use a module use the [[Quickstart/Using Modules| Quickstart]].
 
If you are looking for how to use a module use the [[Quickstart/Using Modules| Quickstart]].
 +
 +
An up-to-date list of all modules available on Viper can be found at [https://hpc.hull.ac.uk/upload/module.html Module List]
  
 
Click on the links below for support on the individual applications:
 
Click on the links below for support on the individual applications:
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| Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler.
 
| Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler.
 
|-  
 
|-  
−
| Albacore
+
| [[applications/Miniconda|Anaconda]]
−
| Albacore is a software project that provides an entry point to the Oxford Nanopore basecalling algorithms
+
| Anaconda is the leading open data science platform powered by Python.  
−
|-
 
−
| [[applications/Anaconda|Anaconda]]
 
−
| Anaconda is the leading open data science platform powered by Python. (See also [[Applications/Miniconda|Miniconda]]).
 
 
|-
 
|-
 
| Arnold
 
| Arnold
−
| Renderer.
+
| Monte Carlo ray tracing renderer.
 
|-
 
|-
 
| Autotools
 
| Autotools
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|-
 
|-
 
| [[applications/Bridger|Bridger]]
 
| [[applications/Bridger|Bridger]]
−
| Bridger is an efficient ''de novo'' trascriptome assembler for RNA-Seq data. It can assemble all transcripts from short reads (single or paired) without using a reference.   
+
| Bridger is an efficient ''de novo'' transcriptome assembler for RNA-Seq data. It can assemble all transcripts from short reads (single or paired) without using a reference.   
 
|-
 
|-
 
| [[applications/Centrifuge|Centrifuge]]
 
| [[applications/Centrifuge|Centrifuge]]
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|-  
 
|-  
 
| [[Applications/ffmpeg|ffmpeg]]
 
| [[Applications/ffmpeg|ffmpeg]]
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| FFmpeg is a very fast video and audio converter that can also grab from a live audio/video source.
+
| FFmpeg is a very fast video and audio converter that can also be grabbed from a live audio/video source.
 
|-  
 
|-  
 
| Flex
 
| Flex
Line 100: Line 99:
 
|[[applications/Java|Java]]
 
|[[applications/Java|Java]]
 
| Java is a general-purpose computer programming language that is concurrent, class-based, and object-oriented.
 
| Java is a general-purpose computer programming language that is concurrent, class-based, and object-oriented.
−
|-
 
−
|[[programming/Julia|Julia]]
 
−
| Julia is a high-level general-purpose dynamic programming language that was originally designed to address the needs of high-performance numerical analysis and computational science
 
−
|-
 
−
| [[applications/Likwid|Likwid]]
 
−
|  Likwid is a simple-to-install and uses a tool suite of command-line applications for performance-oriented programmers.
 
 
|-
 
|-
 
| [[Applications/Mafft|Mafft]]
 
| [[Applications/Mafft|Mafft]]
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| [[Applications/Maker|Maker]]
 
| [[Applications/Maker|Maker]]
 
|  MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and create genome databases.
 
|  MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and create genome databases.
−
|-
 
−
| Mathematica
 
−
|  Symbolic mathematical computation program.
 
 
|-
 
|-
 
| [[Applications/Matlab|Matlab]]
 
| [[Applications/Matlab|Matlab]]
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| [[Applications/Mercurial|Mercurial]]
 
| [[Applications/Mercurial|Mercurial]]
 
|  Mercurial is truly distributed, giving each developer a local copy of the entire development history. This way it works independently of network access or a central server. Committing, branching and merging are fast and cheap.
 
|  Mercurial is truly distributed, giving each developer a local copy of the entire development history. This way it works independently of network access or a central server. Committing, branching and merging are fast and cheap.
 +
|-
 +
| [[Applications/modflow|Modflow]]
 +
|  Program and framework developed to provide a platform for supporting multiple models and multiple types of models within the same simulation.
 
|-
 
|-
 
| [[applications/Mpich|Mpich]]
 
| [[applications/Mpich|Mpich]]
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|-  
 
|-  
 
| [[applications/Miniconda|Miniconda]]
 
| [[applications/Miniconda|Miniconda]]
−
| Miniconda is a lite version of anaconda used for creating virtual environments.
+
| Miniconda is a lite version of Anaconda used for creating virtual environments.
 
|-
 
|-
 
| [[applications/Minimap2|Minimap2]]
 
| [[applications/Minimap2|Minimap2]]
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|-
 
|-
 
| [[applications/Netcdf-c|Netcdf-c]]
 
| [[applications/Netcdf-c|Netcdf-c]]
−
|  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.
+
|  NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support creating, accessing, and sharing array-oriented scientific data.
 
|-  
 
|-  
 
| [[applications/Nwchem|Nwchem]]
 
| [[applications/Nwchem|Nwchem]]
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|-  
 
|-  
 
| [[applications/Obitools|Obitools]]
 
| [[applications/Obitools|Obitools]]
−
| The OBITools package is a set of programs specifically designed for analysing NGS data in a DNA meta-barcoding context, taking into account taxonomic information.
+
| The OBITools package is a set of programs specifically designed for analysing NGS data in a DNA meta-barcoding context, considering taxonomic information.
 
|-  
 
|-  
 
| [[applications/Openfoam|Openfoam]]
 
| [[applications/Openfoam|Openfoam]]
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|[[applications/Qiime2|Qiime2]]
 
|[[applications/Qiime2|Qiime2]]
 
| QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open-source, and community-developed.
 
| QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open-source, and community-developed.
−
|-
 
−
|[[applications/QuantumPackage2|Quantum Package Shell]]
 
−
| Quantum Package is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multi-reference second-order perturbation theory (PT2).
 
 
|-  
 
|-  
 
|[[applications/R|R]]
 
|[[applications/R|R]]
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|  [[applications/STAR|STAR]]
 
|  [[applications/STAR|STAR]]
 
|  Ultrafast universal RNA-seq aligner.
 
|  Ultrafast universal RNA-seq aligner.
 +
|-
 +
|  [[applications/Star-ccm+|Star-ccm+]]
 +
|  Star-ccm+ package.
 
|-
 
|-
 
| [[applications/Tophat|Tophat]]
 
| [[applications/Tophat|Tophat]]
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==Libraries==
 
==Libraries==
−
Library software listed here refers to those listed in the libs section of typing module avail.
+
Library software listed here refers to those listed in the libs section of the typing module avail.
 
{| class="wikitable mw-collapsible"
 
{| class="wikitable mw-collapsible"
 
| style="width:25%; background: #f5a091;" | <Strong>Library</Strong>
 
| style="width:25%; background: #f5a091;" | <Strong>Library</Strong>
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|-  
 
|-  
 
| [[applications/Parmetis|Parmetis]]
 
| [[applications/Parmetis|Parmetis]]
−
|  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.
+
|  ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, and meshes, and for computing fill-reducing orderings of sparse matrices.
 
|-
 
|-
 
|[[applications/Qt|Qt]]
 
|[[applications/Qt|Qt]]
−
| Qt is a cross-platform framework, that is usually used as a graphical toolkit, although it is also very helpful in creating CLI applications on Viper.
+
| Qt is a cross-platform framework, usually used as a graphical toolkit, although it is also very helpful in creating CLI applications on Viper.
 
|-
 
|-
 
| [[applications/Zlib|Zlib]]
 
| [[applications/Zlib|Zlib]]
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==Test Modules==
 
==Test Modules==
−
The test-modules module does not provide access to a specific application, instead, it provides access to a further set of modules that are in a development state. These modules should not be relied on to be stable modules and are subject to change as software installations are tuned. If you request an application to be installed, we may ask you to test the module while it is in the test-modules area before we make it widely available as a standard module.
+
The test-modules module does not provide access to a specific application, instead, it provides access to a further set of modules that are in a development state.  
 +
 
 +
These modules should not be relied on to be stable modules and are subject to change as software installations are tuned.
 +
 
 +
If you request an application to be installed, we may ask you to test the module while it is in the test modules area before we make it widely available as a standard module.
  
 
<pre style="background-color:#000000; color: white; font-family: monospace, sans-serif;">
 
<pre style="background-color:#000000; color: white; font-family: monospace, sans-serif;">

Latest revision as of 09:42, 21 November 2023

Back to Further Topics

Applications

The following is a list of core applications installed on Viper, with links to further information on using those applications on Viper. If you are looking for an application that requires a special license visit: Applications requiring special licenses.

If you are looking for how to use a module use the Quickstart.

An up-to-date list of all modules available on Viper can be found at Module List

Click on the links below for support on the individual applications:

Package Description
ABySS Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler.
Anaconda Anaconda is the leading open data science platform powered by Python.
Arnold Monte Carlo ray tracing renderer.
Autotools Autotools, is a suite of programming tools designed to assist in making source code packages portable. Provides common tools such as m4-1.4.17, autoconf-2.69, automake-1.15, flex-2.6.2, libtool-2.4, gettext-0.19.8.1, bison-3.0.4 .
BayesTraits 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.
Bison Bison, is a parser generator that is part of the GNU Project.
Blender Blender is a free and open-source 3D creation suite. It supports the entirety of the 3D pipeline—modelling, rigging, animation, simulation, rendering, compositing and motion tracking, and even video editing and game creation.
Bowtie1 The aligner is typically used with short reads and a large reference genome, or for whole-genome analysis. Bowtie is promoted as an ultrafast, memory-efficient short aligner for short DNA sequences.
Bowtie2 Bowtie 2 is more suited to finding longer, gapped alignments in comparison with the original Bowtie1 method.
Bridger Bridger is an efficient de novo transcriptome assembler for RNA-Seq data. It can assemble all transcripts from short reads (single or paired) without using a reference.
Centrifuge Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labelling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem.
CMake CMake is cross-platform free and open-source software for managing the build process of software using a compiler-independent method.
Crop CROP is an unsupervised nucleic acid sequence clustering algorithm. The algorithm sees the OTUs as a Gaussian mixture and models the clustering process using Birth-death MCMC. This approach makes the OTU prediction more accurate.
CP2K CP2K is a quantum chemistry and solid-state physics software package that can perform atomistic simulations of solid-state, liquid, molecular, periodic, material, crystal, and biological systems.
CUDA CUDA is NVIDIA’s parallel computing architecture that enables dramatic increases in computing performance by harnessing the power of the GPU nodes.
Cufflinks Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
Delft3D Delft3D is a world-leading 3D modelling suite to investigate hydrodynamics, sediment transport and morphology and water quality for fluvial, estuarine and coastal environments.
FDS-SMV Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. Smokeview (SMV) is a visualization program used to display the output of FDS and CFAST simulations.
ffmpeg FFmpeg is a very fast video and audio converter that can also be grabbed from a live audio/video source.
Flex Flex (Fast lexical analyser), Flex is a tool for generating scanners: programs that recognize lexical patterns in text.
Fiji Fiji Is Just ImageJ—a "batteries-included" distribution of ImageJ which includes many useful plugins contributed by the community.
gcc GCC (GNU Compiler Collection) is a collection of compilers consisting of C, C++, Fortran and more.
GNUplot Gnuplot is a portable command-line-driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms.
Grace Grace is a WYSIWYG 2D plotting tool for the X Window System and M*tif. Grace is a descendant of ACE/gr, also known as Xmgr.
Guppy Local accelerated basecalling for Nanopore data.
HyPhy HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning.
Intel Parallel Studio Intel Parallel Studio is a software development product that facilitates native code development on Viper in C, C++ and Fortran for parallel computing.
IQtree stochastic algorithm to reconstruct phylogenetic trees using maximum likelihood.
Java Java is a general-purpose computer programming language that is concurrent, class-based, and object-oriented.
Mafft MAFFT is a multiple sequence alignment program for Unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), and FFT-NS-2 (fast; for alignment of <∼30,000 sequences).
Maker MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and create genome databases.
Matlab Numerical Computing Environment.
Mercurial Mercurial is truly distributed, giving each developer a local copy of the entire development history. This way it works independently of network access or a central server. Committing, branching and merging are fast and cheap.
Modflow Program and framework developed to provide a platform for supporting multiple models and multiple types of models within the same simulation.
Mpich MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard.
Miniconda Miniconda is a lite version of Anaconda used for creating virtual environments.
Minimap2 Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.
Mono .NET Framework-compatible set of tools including, among others, a C# compiler and a Common Language Runtime.
MrBayes MrBayes: Bayesian Inference of Phylogeny
Mvapich2 MVAPICH2 is a BSD-licensed implementation of the MPI standard with support for Intel Omni-Path is a high performance.
Ncbi blast It finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
Netcdf-c NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support creating, accessing, and sharing array-oriented scientific data.
Nwchem NWChem provides computational chemistry tools and particularly large scientific computational chemistry problems.
Obitools The OBITools package is a set of programs specifically designed for analysing NGS data in a DNA meta-barcoding context, considering taxonomic information.
Openfoam OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics.
Orca ORCA is a flexible, efficient and easy-to-use general-purpose tool for quantum chemistry with a specific emphasis on the spectroscopic properties of open-shell molecules.
Packmol PACKMOL creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short-range repulsive interactions do not disrupt the simulations.
Paraview ParaView is an open-source, multi-platform data analysis and visualisation application. ParaView users can quickly build visualisations to analyse their data using qualitative and quantitative techniques.
Perl Perl is a flexible high-level, general-purpose, interpreted, dynamic programming language with a large number of libraries.
Prinseq-lite PRINSEQ can be used to filter, reformat, or trim genomic and metagenomic sequence data.
Python Python is a family of high-level, general-purpose, interpreted, dynamic programming languages and includes IPython.
Qiime2 QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open-source, and community-developed.
R R is an open-source programming language and software environment for statistical computing and graphics.
RaXML RaXML is an open-source tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.
Readline GNU Readline is a software library that provides line-editing and history capabilities for interactive programs with a command-line interface, such as Bash.
RStudio RStudio provides popular open-source and enterprise-ready professional software for the R statistical computing environment.
Samtools Tools (written in C using htslib) for manipulating next-generation sequencing data
Savu Python package to assist with the processing and reconstruction of parallel-beam tomography data.
Scalapack The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers
Siesta SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.
STAR Ultrafast universal RNA-seq aligner.
Star-ccm+ Star-ccm+ package.
Tophat It is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyses the mapping results to identify splice junctions between exons.
Transabyss Software pipeline for analysing ABySS-assembled transcriptome contigs
Transrate Transrate is software for de-novo transcriptome assembly quality analysis
Trinityrnaseq Trinity assembles transcript sequences from Illumina RNA-Seq data.
Utilities General utility module including zip, wget and git utilities.
Voxfe VOX-FE is voxel-based FE software with a sophisticated graphical user interface that allows the complex loading regimes that are inevitably present in bio-mechanical analyses to be readily applied to the model geometry, and the resultant 3D stress and strain patterns to be visualised easily.
Yt yt supports structured, variable-resolution meshes, unstructured meshes, and discrete or sampled data such as particles. Focused on driving physically meaningful inquiry, yt has been applied in domains such as astrophysics, seismology, nuclear engineering, molecular dynamics, and oceanography.

Libraries

Library software listed here refers to those listed in the libs section of the typing module avail.

Library Description
Boost C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications.
Cuda CUDA is a parallel computing platform and application programming interface (API) model created by Nvidia.
Expat Expat XML parser library in C
Fftw3 FFTW is a C subroutine library for computing the Discrete Fourier Transform (DFT).
Gsl The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.
Hdf5 HDF5 is a data model, library, and file format for storing and managing data.
Hypre A library of high-performance preconditioners and solvers featuring multi-grid methods for the solution of large, sparse linear systems of equations on massively parallel computers.
Libbeagle BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.
Libgd The module LibGD is an open-source code library for the dynamic creation of images.
Libjpeg-turbo The module Libjpeg-turbo is a JPEG image codec that uses SIMD instructions (MMX, SSE2, AVX2, NEON, AltiVec) to accelerate baseline JPEG compression and decompression
Libpng The reference library for use in applications that read, create, and manipulate PNG (Portable Network Graphics) raster image files.
Ncurses ncurses (new curses) is a programming library providing an application programming interface (API) that allows the programmer to write text-based user interfaces in a terminal-independent manner.
OpenACC OpenACC is an implementation of multithreading, a method of parallelizing whereby a master thread (a series of instructions executed consecutively) forks a specified number of slave threads and the system divides a task among them. This is similar to OpenMP but has had CPU/GPU support from the beginning. There is language support from C/C++ and Fortran.
Openblas OpenBLAS is an optimized BLAS library (based on GotoBLAS2 1.13 BSD version).
OpenCL A framework for writing programs that execute across heterogeneous platforms consisting of central processing units (CPUs), graphics processing units (GPUs), digital signal processors (DSPs), and field-programmable gate arrays (FPGAs) and other processors or hardware accelerators.
OpenMP OpenMP is an implementation of multithreading, a method of parallelizing whereby a master thread (a series of instructions executed consecutively) forks a specified number of slave threads and the system divides a task among them. There is language support from C/C++ and Fortran.
OpenMPI Open MPI is a Message Passing Interface (MPI) library used for communicating between HPC nodes.
Parmetis ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, and meshes, and for computing fill-reducing orderings of sparse matrices.
Qt Qt is a cross-platform framework, usually used as a graphical toolkit, although it is also very helpful in creating CLI applications on Viper.
Zlib zlib is a software library used for data compression.

Test Modules

The test-modules module does not provide access to a specific application, instead, it provides access to a further set of modules that are in a development state.

These modules should not be relied on to be stable modules and are subject to change as software installations are tuned.

If you request an application to be installed, we may ask you to test the module while it is in the test modules area before we make it widely available as a standard module. 

[username@login01 ~]$ module add test-modules
[username@login01 ~]$ module avail
--------------------------------------------------- /usr/share/Modules/modulefiles ----------------------------------------------------
dot         module-git  module-info modules     null        use.own

--------------------------------------------- /trinity/clustervision/CentOS/7/modulefiles ---------------------------------------------
abyss/1.5.2/gcc-4.9.3                   gsl/gcc/2.1                             java/jdk1.8.0_102                       ospray/0.10.1
<standard output>
-------------------------------------------- /trinity/clustervision/CentOS/7/test-modules ---------------------------------------------
SAS/9.4                 gettext/gcc/0.19.8.1          netcdf-c/intel/intelmpi/4.4.1
ansys/v170_test         glib/gcc/2.50.2               netcdf-f/intel/intelmpi/4.4.4
ansys/v172sj            grackle/gcc/serial/2.2        ood/anaconda/2021.11
cairo/1.14.6            harfbuzz/gcc/1.3.3            openfoam-org/10.0/openmpi-4.0.5/gcc-7.3.0    
comsol/52a              libffi/gcc/3.2.1              pango/1.40.3
comsol/53               libxml2/gcc/2.9.4             pcre/gccc/8.38
comsol/53a              matlab/2021a                  pixman/0.34.0
comsol/54               matlab/test                   ruby/2.3.1
enzo/gcc/2016-09-28     mercurial/3.9.1-2016-09-28    singularity/3.5.3/gccc-8.2.0
fontconfig/gcc/2.12.1   mpich/3.2/gcc-5.2.0           scotch/7.0.1/openmpi-4.05/gcc-7.3.0
fontconfig/gcc/2.8.0    music/gcc/1.53                transabyss/1.5.5
freetype/2.7            nas./gcc/2.12.02



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