Software Resources
Overview
Puma, Ocelote, and ElGato are built on CentOS 7 which is the foundation for all compilers, libraries, and applications available on the systems. The same software applications are available on all three supercomputers as they are presented from a unified filesystem.
Many popular software packages are installed and available to the user community as software modules. The short explanation is that loading a module configures your environment so that you do not need to know where it is installed and can begin using the software immediately as soon as it's loaded.
Frequently, different versions of the same software are available as different modules. If you load software without specifying the version, the default in most cases is the latest. For example, "module load julia" will provide Julia version 1.8.5 (at the time of writing), whereas "module load julia/1.6.1" will make an older version available.
Most software that needed to be compiled has used GCC version 8.3. It was the latest available when the software builds were started in 2020. Some other packages are built with the Intel compiler. Both are available to compile your own code. Note that GCC is loaded by default along with OpenMPI 3 (named gnu8 and openmpi3 respectively).
You may request that additional applications be installed if they have general usefulness.
Installed Software
- The list here is usually incomplete because of the frequent changes.
- Some modules are in the operating system also, but are too downlevel, like curl or libtool.
- The current list of modules is available on each compute node with the command "module avail". Not on login nodes.
- Module commands are available here.
| Software | Description |
|---|---|
| Abaqus | Finite element analysis |
| Abyss | Parallel assembler for short read sequence data |
| Admixture | A software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. |
| AmgX | AmgX provides a simple path to accelerated core solver technology on NVIDIA GPUs. AmgX provides up to 10x acceleration to the computationally intense linear solver portion of simulations, and is especially well suited for implicit unstructured methods. |
| Amira | Powerful, multifaceted 2D–5D software for visualization, processing and analysis of microscopy imaging serving Life and Biomedical Sciences. |
| Anaconda | Platform for data science and machine learning |
| Anchorwave | (Anchored Wavefront Alignment) identifies collinear regions via conserved anchors |
| Ansys | Licensed: General purpose finite element modeling package |
| Ant | JAVA build tool |
| ANTLR | ANTLR (ANother Tool for Language Recognition) is a powerful parser generator for reading, processing, executing, or translating structured text or binary files. It's widely used to build languages, tools, and frameworks. From a grammar, ANTLR generates a parser that can build and walk parse trees. |
| AOCL | AMD Optimized CPU Libraries. Includes BLIS, libFLAME, FFTW, LibM, ScaLAPACK |
| Argtable | An ANSI C library for parsing GNU style command line options |
| Aria2 | A lightweight multi-protocol & multi-source command-line download utility |
| Atlas | Automatically Tuned Linear Algebra Software (ATLAS). C and Fortran77 interfaces to a portably efficient BLAS implementation, as well as a few routines from LAPACK |
| Augustus | Gene prediction and is required for Maker |
| Autoconf | GNU tool for producing configure scripts for building, installing and packaging software on computer systems where a Bourne shell is available |
| Autotools | GNU suite of tools to make source code packages portable to many Unix-like systems |
| AWS CLI | CLI tool for interfacing with Amazon Web Services (AWS) |
| Bamtools | C++ API and toolkit for analyzing and managing BAM files |
| Bbmap | Short read aligner for DNA and RNA-seq data |
| Bcftools | A set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF |
| Beagle-lib | Phylogenetics - works with Beast |
| Beast | Bayesian analysis of molecular sequences |
| Bedops | 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 |
| Bedtools | Utilities for comparing, summarizing and intersecting genomic features in the UCSC Genome Browser BED format |
| Biocontainers | Biocontainers is a registry of Biology tools that can be pulled from a Docker container into a Singularity container. |
| Bismark | A program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step |
| Bison | General purpose parser generator that converts a grammar description for an LALR(1) context-free grammar into a C program to parse that grammar. |
| Blas | Basic Linear Algebra Subprograms |
| Blast | Search tool that finds regions of local similarity between nucleotide or protein sequences |
| Blat | Alignment tool like BLAST, but structured differently |
| Blender | 3D Visualization software |
| Boost | Peer reviewed C++ source libraries |
| Bowtie2 | Ultrafast, memory-efficient tool for aligning sequencing reads to long reference sequences. |
| BWA | Fast light-weight tool that aligns relatively short sequences to a sequence database |
| Caffe | Deep learning framework made with expression, speed, and modularity |
| Canu | Fork of the Celera Assembler designed for high-noise single-molecule sequencing |
| CASTEP | CASTEP is a full-featured materials modelling code based on a first-principles quantum mechanical description of electrons and nuclei. It uses the robust methods of a plane-wave basis set and pseudopotentials. |
| CCP | Cisco Configuration Professional is a GUI based device management tool for Cisco access routers. |
| Centrifuge | Classifier for metagenomic sequences. |
| CDO | Climate Data Operator is a collection of command-line Operators to manipulate and analyze Climate and NWP model Data |
| CellRanger | A set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering. |
| Cern-Root | A modular scientific software framework |
| Cfitsio | A library of subroutines for data files. Available on each compute node not as a module. |
| Chimera | An extensible molecular modeling system |
| Chapel | Programming language designed for productive parallel computing at scale |
| Clustal Omega | Clustal Omega is a multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences |
| Cluster | The open source clustering software implements the most commonly used clustering methods for gene expression data analysis |
| ClusterShell | ClusterShell is an event-driven open source Python library, designed to run local or distant commands in parallel on server farms or on large Linux clusters |
| Cmake | Tool to control the compilation process. "cmake" comes with the operating system, but it is an old version 2. Likely you should "module load cmake" which will get you a much newer release of version 3. |
| Comsol | Modeling and simulating physics-based problems (licensed) |
| Contig-extender | Developed to extend contigs, complementing de novo assembly. |
| Contrib | Adds user supported software to your module path. On Ocelote this is /unsupported |
| Coot | Macromolecular model building |
| CP2K | Open Source Molecular Dynamics |
| Cplex | IBM optimization models, combining leading solver engines with a tightly integrated IDE and modeling language |
| Crest | An IO-based scheduler for semiempirical quantum mechanical calculations at the GFNn-xTB level. |
| Cuda | Parallel computing platform and API model for Nvidia GPU's |
| Cufflinks | Assembles transcripts, estimates their abundances, tests for differential expression and regulation in RNA-Seq samples |
| Curl | Computer software project providing a library and command-line tool for transferring data using various protocols |
| dealii | deal.II is a C++ program library targeted at the computational solution of partial differential equations using adaptive finite elements |
| Diamond | Alignment tool for aligning short DNA sequencing reads to a protein reference database |
| Difx | Software correlator used to process the simulated files |
| DMTCP | A tool to transparently checkpoint the state of multiple simultaneous applications, including multi-threaded and distributed applications. |
| Eagle | Estimates haplotype phase either within a genotyped cohort or using a phased reference panel |
| EggNOG-mapper | A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. |
| Eigen | high-level C++ library of template headers |
| Energyplus | A whole building energy simulation program that engineers, architects, and researchers |
| Exonerate | Generic tool for sequence comparison |
| Fastme | Algorithms to infer phylogenies |
| FastQC | Quality control tool for high throughput sequence data |
| Fasttree | For large alignments |
| FastX | Command line tools for Short-Reads FASTA/FASTQ files preprocessing |
| FFmpeg | A cross-platform solution to record, convert and stream audio and video |
| FFTW | Fast fourier transforms. Ocelote has multiple versions |
| Fiji | Fiji is an image processing package—a “batteries-included” distribution of ImageJ2, bundling a lot of plugins which facilitate scientific image analysis. |
| FreeBayes | Bayesian genetic variant detector designed to find small polymorphisms |
| Freec | Quantifying transcripts |
| Freesurfer | Analysis of neuroimaging data |
| Gamess | A program for ab initio quantum chemistry |
| GATK | Identifying SNPs and indels in germline DNA from Broad Institute |
| Gaussian | Electronic structure program. Licensed for general use |
| GDAL | a computer software library for reading and writing raster and vector geospatial data formats |
| GenomeTools | The versatile open source genome analysis software |
| GEOS | Geometry Engine Open Source |
| Git | Version control system (VCS) for tracking changes in computer files and coordinating work on those files among multiple people. |
| GLPK | The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP) and mixed integer programming (MIP) |
| Gnuplot | Generates two- and three-dimensional plots of functions |
| Go | Programming language from Google |
| Gotcha | A library that provides function wrapping, interposing a wrapper function between a function and its callsites. |
| Grace | Grace is a Motif application for two-dimensional data visualization. Grace can transform the data using free equations, FFT, cross- and auto-correlation |
| Gromacs | Molecular dynamics software primarily designed for biomolecular systems |
| GSL | The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers |
| Gurobi | Mathematical problem solver for prescriptive analytics |
| HDF5 | Data model, library, and file format for storing and managing data (built with GCC and Intel) |
| HISAT2 | A fast and sensitive alignment program for mapping next-generation sequencing reads. Replaces TopHat |
| HMMER | Biosequence analysis using profile hidden Markov models |
| Hotpants | High Order Transform of Psf ANd Template Subtraction code (hotpants) |
| hpctoolkit hpctraceviewer hpcviewer | Tools for measurement and analysis of program performance |
| htslib | Unified C library for accessing common file formats. Also part of samtools |
| hwloc | Gathers information about parallel computing platforms so as to exploit them efficiently |
| HYPRE | Library of linear solvers featuring parallel multigrid |
| IDL | Interactive Data Language, is a programming language used for data analysis, particularly in astronomy. Special case: restricted to licensed users |
| iGraph | Routines for simple graphs and network analysis |
| Intel Compilers | Licensed compilers |
| Intel MPI | Intel MPI (integrated from 2019 on) |
| Intel Toolkit | Intel DAAL, GDB, IPP, MKL, TBB, Intel-Cluster (integrated from 2019 on) |
| IQ-TREE | Efficient phylogenetic software |
| iRods | Client - open source data management |
| Jags | Analysis of Bayesian hierarchical models using Markov Chain Monte Carlo simulation |
| Java | Programming language |
| Jellyfish | Fast, memory-efficient counting of k-mers in DNA. Used by Trinity |
| Julia | High-level, high-performance dynamic programming language for technical computing |
| Jupyter | Jupyter notebooks are available at the web service OnDemand |
| Kallisto | Quantifying abundances of transcripts from RNA-Seq data |
| LAMMPS | Classical molecular dynamics code |
| LAMMPS KOKKOS | Accelerator package for LAMMPS using data structures and macros provided by the Kokkos library |
| LAPACK | Numerical linear algebra |
| Libmesh | The libMesh library provides a framework for the numerical simulation of partial differential equations using arbitrary unstructured discretizations |
| Libpng | libpng is the official PNG reference library. It supports almost all PNG features, is extensible, and has been extensively tested |
| Libtool | Generic library building tool |
| LS-OPT (lsopt) | Design optimization |
| MAFFT | Multiple sequence alignment program |
| Maker | Portable and easily configurable genome annotation pipeline |
| Mathematica | Licensed: A single integrated, continually expanding system that covers the breadth and depth of technical computing |
| MATLAB | High-level language and interactive environment, performs computationally intensive tasks |
| Maven | A build automation tool used primarily for Java projects |
| MCL | A cluster algorithm for graphs |
| Meme | Suite of motif-based sequence analysis tools |
| MetaPhlAn | A computational tool for profiling the composition of microbial communities |
| Midnightcommander | A visual file manager |
| Migrate | Software that estimates population parameters, effective population sizes and migration rates of n populations, using genetic data |
| Moose | An open-source parallel finite element framework |
| Mothur | Software for microbial biology |
| Mrbayes | Provides bayesian estimation of phylogeny |
| MPICH/2 | Freely available, portable implementation of MPI. Renamed to MPICH |
| MVAPICH | Library exploiting novel features and mechanisms of high-performance networking technologies |
| Mummer | Rapid whole genome alignment |
| NAMD | Molecular dynamics. Cuda version is "namd-cuda" |
| NCBI-vdb | A collection of tools and libraries for using data in the INSDC Sequence Read Archives. |
| NCDU | NCurses Disk usage analyzer |
| NCL (ncl-ncarg) | NCAR Command Language |
| NCO | Toolkit to manipulate and analyze data stored in netCDF format |
| NetCDF | Software libraries and self-describing, machine-independent data formats supporting the creation, access, and sharing of array-oriented scientific data |
| Netlogo | A programmable modeling environment for simulating natural and social phenomena |
| NGS-SDK | A new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. |
| NUFEB | A massively parallel simulator for individual-based modelling of microbial communities |
| OHPC | OpenHPC: Provides a variety of common, pre-built ingredients required to deploy and manage an HPC Linux cluster |
| OligoArrayAux | A subset of the UNAFold package for use with OligoArray |
| Openblas | An optimized BLAS library |
| OpenFOAM | Computational Fluid Dynamics software |
| OpenMPI | High performance message passing library |
| OrthoFinder | Accurate inference of orthogroups, orthologues, gene trees and rooted species |
| Ovito | A visualization and analysis software for output data generated in molecular dynamics, atomistic Monte-Carlo and other particle-based simulations. |
| Pandaseq | A program to align illumina reads |
| Papi | Performance application programming interface |
| Parallel | GNU Parallel is a shell tool for executing jobs in parallel |
| Paraview | ParaView is an open-source, multi-platform data analysis and visualization application. |
| Parflow | A parallel integrated hydrology model |
| ParMETIS | An MPI-based parallel library Integrated in PetSc |
| Pasta | Practical Alignment using Sate and TrAnsitivity. This is installed to python/2. |
| PCRE | A set of functiAons that implement regular expression pattern matching using the same syntax and semantics as Perl 5. |
| Peridigm | Computational peridynamics code from Sandia NL |
| Perl | Programming language |
| PETSc | A suite of data structures and routines developed by Argonne National Laboratory for the scalable (parallel) solution of scientific applications modeled by partial differential equations. The default version is built with GCC and real arithmetic. There are other modules built with Intel compilers and complex arithmetic support. |
| PGI | PGI Compilers and Tools |
| phdf5 | A file format, library, and utility programs for efficiently managing large and complex datasets stored in files. |
| phenix | A comprehensive software package for macromolecular structure determination using crystallographic (X-ray, neutron and electron) and electron cryo-microscopy |
| Photoscan-pro | Performs photogrammetric processing of digital images and generates 3d spatial data |
| Picard | Command line tools for manipulating high-throughput sequencing |
| pkg-config | A computer program that defines and supports a unified interface for querying installed libraries for the purpose of compiling software that depends on them |
| Plasma | Parallel Linear Algebra Software for Multicore Architectures |
| Plink | Whole genome association analysis toolset |
| pmix | A means of exchanging wireup information needed for interprocess communication |
| pnetcdf | A high-performance parallel I/O library for accessing Unidata's NetCDF, files in classic formats, specifically the formats of CDF-1, 2, and 5. |
| Proj | Cartographic projections and coordinate transformations library |
| Python | Object-oriented programming language We encourage the use of virtualenv to build your own environment. |
| Qctool | Software to filter out samples or variants |
| Qiime | Quantitative Insights Into Microbial Ecology. Qiime2 is a package in Python3 |
| Quantum-espresso | Materials modeling |
| R | Language and environment for statistical computing and graphs |
| RStudio | RStudio is an IDE for R, available at OnDemand web services |
| RAxML | A program for sequential and parallel Maximum Likelihood-based inference of large phylogenetic trees |
| Relion | Program for Maximum A Posteriori refinement in cry-electron microscopy |
| Remora | Resource Monitoring for Remote Applications |
| RepeatMasker | A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences |
| Rings | "Rigorous Investigation of Networks Generated using Simulations" is a scientific code developed in Fortran90/MPI to analyze the results of molecular dynamics simulations |
| Rmblast | A RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler |
| Root-Cern | A modular scientific software framework |
| Ruby | A dynamic, reflective, object-oriented, general-purpose programming language. |
| Sagemath | A free open-source mathematics software system |
| Salmon | A quasi-mapping bioinformatics tool |
SAMRAI | Library to explore application, numerical, parallel computing, and software issues associated with structured adaptive mesh refinement (SAMR) |
| SAMTools | Utilities for manipulating alignments in SAM format |
| SAS | Software suite developed by SAS Institute for advanced analytics, multivariate analyses, business intelligence, data management, and predictive analytics. |
| SBT | Scala build tool |
| Scala | General-purpose programming language |
| ScaLAPACK | Scalable LAPACK |
| Schrodinger | Licensed: Molecular modeling and materials science. |
| Seqlogo | Package that takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo. |
| Shapeit | Estimation of phasing for SNP sequencing data |
| Signalp | Package that predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. |
| Silo | A mesh and field I/O library and scientific database |
| Singularity | Singularity containers let users run applications in a Linux environment of their choosing. See tutorial information |
| Slim | An evolutionary simulation software package used for research and teaching |
| SNAP | Used by Maker |
| SOAPdenovo2 | A novel short-read assembly method |
| SPAdes | St. Petersburg genome assembler, for both standard isolates and single-cell MDA bacteria assemblies |
| Sparsehash | An extremely memory-efficient hash_map implementation |
| Spark | From Apache. Open-source distributed general-purpose cluster computing framework |
| Spectra | C++ library for large scale eigenvalue problems |
| Speedseq | An open-source genome analysis platform for rapid genome analysis and interpretation |
| Spparks | Kinetic Monte Carlo simulator from Sandia |
| SRAtoolkit | Enables reading of sequencing files from the SRA database. From NCBI |
| Stacks | Software pipeline for building loci from short-read sequences |
| Star | RNA-seq Aligner |
| Starfusion | Uses the STAR aligner to identify candidate fusion transcripts |
| SuperLU | A general purpose C (also callable from Fortran) library for the direct solution of large, sparse, nonsymmetric systems of linear equations |
| Tmhmm | Package that predicts transmembrane helices in proteins. |
| TopHat | Fast splice junction mapper for RNA-Seq reads |
| TRF | Telomere Restriction Fragment (TRF) Analysis |
| Trilinos | Set of solvers from Sandia National Labs |
| Trimmomatic | A flexible trimmer for illumina sequence data |
| Trinity | Package which enables the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data |
| Trinotate | Annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes |
| VASP | Atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. Special case: restricted to licensed users |
| VCFtools | Tool providing easily accessible methods for working with complex genetic variation data in the form of VCF files |
| Velvet | De novo genomic assembler specially designed for short read sequencing technologies |
| Visit | Interactive parallel visualization and graphical analysis tool for viewing scientific data |
| Vtune | Intel performance profiler (vtune_amplifier_xe) |
| WGS | Whole Genome Shotgun Assembler for the reconstruction of genomic DNA sequence from WGS sequencing data |
| Wham | Whole genome Alignment Metrics |
| Wien2K | Software for electronic structure calculations using DFT |
| WRF WPS | Weather Research and Forecasting Model. Special case: available to Hydrology and Atmospheric Sciences |
| XDMF | eXtensible Data Model and Format |
| Xz | Free general-purpose data compression software with a high compression ratio. |
| zlib | A software library used for data compression. |
** installed on the operating system of each node. "module load xx" is not necessary.