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Available Software
'module command shows a list of available software and set-up environment variables.
Below are some of the software programs installed on Cypress.
Compiler and Programming Environment
| name | description | URL | license | installed version (As of Jun 2026) |
|---|---|---|---|---|
| Anaconda | distribution of the Python and R programming languages for scientific computing | https://www.anaconda.com/ | free | 2.1.0, 2.5.0, 2018.12, 2019.03, 2020.07, 2023.07, 4.0.0, 5.1.0 |
| gcc | GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, Go, D and Modula-2 as well as libraries for these languages. | https://gcc.gnu.org/ | GPL | 4.7.4, 4.9.4, 6.3.0, 8.5.0, 9.5.0 |
| Intel-psxe | Parallel Studio is composed of several component parts, Intel C/C++/Fortran compiler with OpenMP. Math Kernel Library (MKL), Intel MPI Library, etc. | https://www.intel.com/ | commercial | 2015-update1(default), 2016, 2019-update1 |
| OpenJDK | Open-source implementation of the Java Platform Standard Edition (Java SE) and Java Development Kit. | https://openjdk.org/ | GPL-2.0 with Classpath Exception | 1.8.0, 17.0.7+7 |
| Mathematica | Technical computing environment for symbolic mathematics, numerical computation, visualization, and scientific programming. | https://www.wolfram.com/mathematica/ | Commercial | 12.0 |
| Matlab | MATLAB is a proprietary multi-paradigm programming language and numeric computing environment developed by MathWorks. | https://www.mathworks.com/products/matlab.html | commercial (site license) | r2017b, r2020a, r2022b, r2023a |
| R | software environment for statistical computing and graphics | https://www.r-project.org/ | Public | 3.1.2, 3.2.4, 3.5.2-intel, 3.6.1-intel, 4.1.0-intel, 4.1.1-intel, 4.3.2, 4.4.1 |
| SAS | statistical software suite | https://www.sas.com/ | Commercial (site license) | 9.4 |
| Stata | Stata is a general-purpose statistical software package developed by StataCorp for data manipulation, visualization, statistics, and automated reporting. | https://www.stata.com/ | commercial (site license (sequential version only)) | 15-site_lic |
Bioinformatics Tools
| name | description | URL | license | installed version (As of Jun 2026) |
|---|---|---|---|---|
| AFNI | Software suite for analysis, visualization, and processing of functional and structural neuroimaging data. | https://afni.nimh.nih.gov/ | Public Domain | 23.0.06 |
| Angsd | analyzing NGS data | https://www.popgen.dk/angsd/index.php/ANGSD | Public | 0.941 |
| Bcftools | programs for interacting with high-throughput sequencing data | https://samtools.github.io/bcftools/ | public | 1.16, 1.21 |
| Bcl2fastq2 | demultiplex data and convert Illumina BCL files to FASTQ file formats | https://emea.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html | MIT | 2.20 |
| BCL Convert | Illumina software for converting BCL sequencing output into FASTQ files and associated metrics. | https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html | Commercial | 4.1.7 |
| Bedops | fast, highly scalable and easily-parallelizable genome analysis toolkit | https://github.com/bedops/bedops | GPL-2 | 2.4.41 |
| Bedtools2 | a powerful toolset for genome arithmetic. | https://bedtools.readthedocs.io/en/latest/ | MIT | 2.27.1, 2.30.0 |
| bowtie | an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences | https://bowtie-bio.sourceforge.net/bowtie2/index.shtml | public | 1.1.1, 2.5.1 |
| Bwa | software package for mapping low-divergent sequences against a large reference genome, such as the human genome | https://bio-bwa.sourceforge.net/ | GPL-3 | 0.7.15, 0.7.17 |
| Cellranger | A set of analysis pipelines that perform sample demultiplexing, barcode processing, single cell 3' and 5' gene counting, V(D)J transcript sequence assembly and annotation, and Feature Barcode analysis from single cell data. | https://www.10xgenomics.com/software | limited | 6.0.0, 7.1.0 |
| Cell Ranger ARC | Pipeline for joint analysis of chromatin accessibility and gene expression in single cells. | https://www.10xgenomics.com/support/software/cell-ranger-arc/latest/getting-started/what-is-cell-ranger-arc | Commercial | 1.0.1 |
| Cellranger-ATAC | Software application for analyzing and visualizing Epi ATAC (formerly Single Cell ATAC) data produced by the 10x Genomics Chromium platform | https://www.10xgenomics.com/support/software/cell-ranger-atac/latest | limited | 2.0.0 |
| Cufflinks | Transcriptome assembly and differential expression analysis for RNA-Seq data. | http://cole-trapnell-lab.github.io/cufflinks/ | Boost Software License | 2.2.1 |
| DELLY | Structural variant discovery tool using paired-end and split-read sequencing signals. | https://github.com/dellytools/delly | BSD-3-Clause | 1.2.6 |
| Entrez Direct | Command-line tools for accessing and querying NCBI Entrez biological databases. | https://www.ncbi.nlm.nih.gov/books/NBK179288/ | Public Domain | 2025 |
| fastp | Fast all-in-one FASTQ preprocessing tool. | https://github.com/OpenGene/fastp | MIT | 0.23.4 |
| FastQC | Quality control tool for high throughput sequence data. | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | GPL | 0.11.7, 0.12.1 |
| fastStructure | Efficient Bayesian framework for inferring population structure from genotype data. | https://github.com/rajanil/fastStructure | Open Source | 1.0 |
| Gatk | Genome Analysis Toolkit | https://gatk.broadinstitute.org/hc/en-us | public | 4.1.8.1, 4.5.0.0 |
| gdc-client | Genomic Data Commons (GDC) data transfer tool. The gdc-client provides several convenience functions over the GDC API which provides general download/upload via HTTPS. | https://github.com/NCI-GDC/gdc-client | public | 1.6.1 |
| GRIDSS | Genomic Rearrangement IDentification Software Suite for structural variant and genomic rearrangement detection. | https://github.com/PapenfussLab/gridss | GPL-3.0 | 2.13.2 |
| Htslib | an implementation of a unified C library for accessing common file formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing data. It is the core library used by samtools and bcftools. | https://www.htslib.org/ | public | 1.13, 1.19, 1.21 |
| Kraken2 | Taxonomic sequence classification system using exact k-mer matches for metagenomic analysis. | https://github.com/DerrickWood/kraken2 | MIT | 2.1.3 |
| LUMPY | Probabilistic framework for structural variant discovery integrating multiple structural variation signals. | https://github.com/arq5x/lumpy-sv | MIT | 0.3.1 |
| MAFFT | Multiple sequence alignment program for nucleotide and protein sequences. | https://mafft.cbrc.jp/alignment/software/ | BSD | 7.505 |
| Manta | Rapid structural variant and indel caller for next-generation sequencing data. | https://github.com/Illumina/manta | Open Source | 1.6.0 |
| MultiQC | Aggregates results from many bioinformatics analyses into a single interactive quality-control report. | https://seqera.io/multiqc/ | GPL-3.0 | 1.14 |
| ncbi-blast | The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. | https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD\=Web&PAGE_TYPE\=BlastHome | public | 2.12.0+, 2.14.1+rmblast |
| NGSUtils | NGSUtils is a suite of software tools for working with next-generation sequencing datasets. | https://ngsutils.org/ | BSD | 0.5.9 |
| Pathway Tools | Software environment for pathway and genome informatics, metabolic pathway analysis, and Pathway/Genome Database construction. | https://bioinformatics.ai.sri.com/ptools/ | Free for academic use | 28.5, 29.5 |
| Picard | Toolkit for manipulating high-throughput sequencing data formats such as BAM and SAM. | https://broadinstitute.github.io/picard/ | MIT | 2.20.7 |
| PLINK | Whole-genome association analysis toolset for genetic and population studies. | https://www.cog-genomics.org/plink/ | Open Source | 1.07, 1.9 |
| pyRAD | pyRAD is commonly employed for RADseq studies at deeper phylogenetic scales, however, it works equally well at shallow scales. | https://github.com/dereneaton/pyrad | GPL | 3.0.66 |
| qiime2 | QIIME 2™ (pronounced “chime two” 🔔) is a microbiome multi-omics bioinformatics and data science platform that is trusted, free, open source, extensible, and community developed and supported. | https://qiime2.org/ | BSD | 2023.2 |
| RepeatMasker | Screens DNA sequences for interspersed repeats and low-complexity regions and generates repeat annotations and masked sequences. | https://www.repeatmasker.org/ | OSL-2.1 | 4.1.7 |
| rMATS-turbo | Fast software for detection and quantification of differential alternative splicing events from RNA-Seq data. | https://github.com/Xinglab/rmats-turbo | BSD-2-Clause | 4.1.1 |
| Rsem | RNA-Seq by Expectation-Maximization | https://deweylab.github.io/RSEM/ | GPL | 1.2.31 |
| SAMBLASTER | Marks duplicate reads and extracts discordant and split-read alignments from SAM files for structural variant analysis. | https://github.com/GregoryFaust/samblaster | MIT | 0.1.26 |
| Samtools | a suite of programs for interacting with high-throughput sequencing data | https://www.htslib.org/ | public | 0.1.17, 0.1.19, 1.10, 1.13, 1.16.1, 1.21, 1.5 |
| Space Ranger | Space Ranger is a set of analysis pipelines that process 10x Genomics Visium data with brightfield or fluorescence microscope images. | https://www.10xgenomics.com/support/software/space-ranger/latest | limited | 2.0.1, 3.0.1 |
| Sratoolkit | The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. | https://hpc.nih.gov/apps/sratoolkit.html | public | 3.0.0 |
| Stacks | software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. | https://catchenlab.life.illinois.edu/stacks/ | GPL | 2.2 |
| star | Spliced Transcripts Alignment to a Reference | https://github.com/alexdobin/STAR | MIT | 2.3.0e, 2.5.2a, 2.7.11b |
| Subread | High-performance toolkit for sequence alignment, read quantification, exon junction detection, and mutation discovery. | https://subread.sourceforge.net/ | GPL-3.0 | 2.1.1 |
| TopHat | Spliced-read mapper for RNA-Seq data that identifies exon-exon splice junctions using Bowtie alignments. | https://ccb.jhu.edu/software/tophat/ | BSL-1.0 | 2.1.1 |
| Tandem Repeats Finder | Identifies and reports tandem repeat sequences in genomic DNA. | https://tandem.bu.edu/trf/trf.html | AGPL-3.0 | 4.09.1 |
| Trimmomatic | Flexible tool for trimming adapters and low-quality bases from Illumina sequencing reads. | http://www.usadellab.org/cms/?page=trimmomatic | GPL-3.0 | 0.39 |
| UCSC Utilities | Command-line utilities from the UCSC Genome Browser project for manipulating, querying, and converting genomic data formats. | https://hgdownload.soe.ucsc.edu/admin/exe/ | Free for academic use | linux.x86_64.v385 |
| VCFtools | Toolkit for filtering, summarizing, comparing, and manipulating Variant Call Format (VCF) files. | https://vcftools.github.io/ | LGPL-3.0 | 0.1.14 |
Computational Chemistry and Physics
| name | description | URL | license | installed version (As of Jun 2026) |
|---|---|---|---|---|
| Gaussian | Starting from the fundamental laws of quantum mechanics, Gaussian 16 predicts the energies, molecular structures, vibrational frequencies and molecular properties of compounds and reactions in a wide variety of chemical environments. | https://gaussian.com/ | commercial (IT purchased DVD) | gaussian09/d.01, gaussian16/g16 |
| Gromacs | molecular dynamics package designed for simulations of proteins, lipids, and nucleic acids. | https://www.gromacs.org/ | public | 2016.3, 2020.7, 2020.7-plumed+indus, 2021.4, 2023.5, 5.1.2 |
| Lammps | Large-scale Atomic/Molecular Massively Parallel Simulator is a molecular dynamics program from Sandia National Laboratories. | https://www.lammps.org/#gsc.tab\=0 | GPL | stable-2Aug2023 |
| Namd2 | a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. | https://www.ks.uiuc.edu/Research/namd/ | public | 2.13b2-MPI-intel-2016, 2.13b2-charmrun-g++-4.4.7 |
| Open Babel | Chemical toolbox for converting, analyzing, and manipulating molecular structure data and file formats. | https://openbabel.org/ | GPL-2.0 | 3.1.1 |
| ORCA | General-purpose quantum chemistry package for electronic structure calculations, spectroscopy, and molecular modeling. | https://www.faccts.de/orca/ | Free for academic use | 6.0.1 |
| PLUMED | PLUMED is an open-source, community-developed library that provides a wide range of different methods. | https://www.plumed.org// | GPL | 2.9.0-indus |
| ROOT | high-energy physics tools | https://root.cern | LGPL v2.1+ | 5.34.36 |
| Rosetta | a software suite of algorithms for computational modeling and analysis of protein structures. | https://rosettacommons.org/software/ | Non-Commercial License | 3.14, 3.9 |
| UDUNITS | Library and utilities for encoding, decoding, and converting scientific units of measure. | https://www.unidata.ucar.edu/software/udunits/ | BSD | 2.2.28 |
Developers Tools and Libraries
| name | description | URL | license | installed version (As of Jun 2026) |
|---|---|---|---|---|
| Armadillo | C++ library for linear algebra & scientific computing | https://arma.sourceforge.net/ | Apache License 2.0 | 12.6.6 |
| Atlas | Automatically Tuned Linear Algebra Software | https://math-atlas.sourceforge.net/ | BSD | 3.10.2 |
| Binutils | collection of binary tools | https://www.gnu.org/software/binutils/ | GPL | 2.37 |
| blcr | Berkeley Lab Checkpoint/Restart | https://crd.lbl.gov/divisions/amcr/computer-science-amcr/class/research/past-projects/BLCR/ | public | 0.8.5 |
| Boost | C++ source libraries | https://www.boost.org/ | Boost Software License | 1.57.0, 1.76.0 |
| Cmake | build system generator | https://cmake.org/ | open-source | 3.0.2, 3.12.1, 3.24.1 |
| eigen | Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. | https://eigen.tuxfamily.org/ | MPL2 | 3.2.4 |
| Fftw | FFTW is a C subroutine library for computing the discrete Fourier transform (DFT). | https://www.fftw.org/ | GPL | 3.3.4 |
| GEOS | Computational geometry library implementing spatial operations used by GIS software. | https://libgeos.org/ | LGPL-2.1 | 3.11.0 |
| Git | Distributed version control system for tracking changes in source code and collaborative software development. | https://git-scm.com/ | GPL-2.0 | 2.4.1 |
| GNU MP | Library for arbitrary-precision arithmetic on integers, rational numbers, and floating-point numbers. | https://gmplib.org/ | LGPL-3.0 / GPL-2.0 | 6.2.1 |
| GSL | The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. | https://www.gnu.org/software/gsl/ | GPL | 2.6 |
| HDF5 | Hierarchical Data Format (HDF) is a set of file formats designed to store and organize large amounts of data. | https://www.hdfgroup.org/solutions/hdf5/ | free | 1.10.5, 1.8.14 |
| jags | (Just Another Gibbs Sampler) statistical analysis of Bayesian hierarchical models by Markov Chain Monte Carlo. | https://mcmc-jags.sourceforge.io/ | GPL2 | 4.3.0 |
| GNU MPC | Library for arbitrary-precision complex arithmetic with correct rounding. | https://www.multiprecision.org/mpc/ | LGPL-3.0+ | 1.2.1 |
| GNU MPFR | Library for multiple-precision floating-point computations with correct rounding. | https://www.mpfr.org/ | LGPL-3.0+ | 4.1.0 |
| MPICH | High-performance and portable implementation of the MPI standard for parallel computing. | https://www.mpich.org/ | MPICH License | 3.1.4 |
| netcdf | 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. | https://www.unidata.ucar.edu/software/netcdf/ | free | 4.3.2 |
| Nextflow | Workflow manager for reproducible pipelines. | https://www.nextflow.io/ | Apache-2.0 | 23.04 |
| OpenBLAS | Optimized BLAS (Basic Linear Algebra Subroutine) library | https://www.openblas.net/ | BSD | 0.3.18 |
| Openmpi | MPI library | https://www.open-mpi.org/ | BSD | 1.8.4, 4.1.6, 5.0.5 |
| OpenSSL | TLS/SSL and crypto toolkit. | https://www.openssl.org/ | Apache-style | 3.5.1 |
| PCRE | Perl Compatible Regular Expressions library for high-performance pattern matching. | https://www.pcre.org/ | BSD | 10.38, 8.39 |
| TRE | POSIX-compliant regular expression library with support for approximate and fuzzy matching. | https://github.com/laurikari/tre | BSD-2-Clause | 0.8.0 |
| valgrind | Valgrind is an instrumentation framework for building dynamic analysis tools. There are Valgrind tools that can automatically detect many memory management and threading bugs, and profile your programs in detail. You can also use Valgrind to build new tools. | https://valgrind.org/ | GPL2 | 3.21.0 |
Utilities and Tools
| name | description | URL | license | installed version (As of Jun 2026) |
|---|---|---|---|---|
| Awscli | AWS Command Line Interface | https://aws.amazon.com/cli/ | Public | 1.29.1 |
| Bash | GNU Bourne Again Shell, a widely used Unix command-line shell and scripting environment. | https://www.gnu.org/software/bash/ | GPL-3.0 | 5.1.8 |
| Bbcp | Securely and quickly copy data from source to target | https://www.slac.stanford.edu/~abh/bbcp/ | GPL | amd64_rhel60 |
| bzip2 | Lossless compression utility and library using the Burrows-Wheeler compression algorithm. | https://sourceware.org/bzip2/ | bzip2 License | 1.0.6 |
| curl | Command-line tool and library for transferring data with URLs across many network protocols. | https://curl.se/ | curl license | 8.11.0 |
| Globus Connect Personal | Create a Globus collection | https://www.globus.org/globus-connect-personal/ | public | 3.2.5 |
| Gnuparallel | command-line utility allows the user to execute shell scripts or commands in parallel. | https://www.gnu.org/software/parallel/ | GPL | 20180322, 20230122 |
| gnuplot | Command-line plotting tool. | http://www.gnuplot.info/ | gnuplot license | 5.0.1 |
| Grace | Interactive scientific graphing and data visualization tool for plotting numerical data. | https://plasma-gate.weizmann.ac.il/Grace/ | GPL | 5.1.25 |
| OpenSSH | Secure shell utilities. | https://www.openssh.com/ | BSD-style | 9.1 |
| Rclone | Rclone is a command-line program to manage files on cloud storage such as Box | https://rclone.org/ | MIT | 1.49.3 |
| Singularity | Apptainer (formerly Singularity) simplifies the creation and execution of containers, ensuring software components are encapsulated for portability and reproducibility. | https://apptainer.org/ | public | 3.9.0 |
| VTK | Visualization Toolkit for 3D computer graphics, image processing, and scientific visualization. | https://vtk.org/ | BSD-3-Clause | 6.1.0 |
| XCrySDen | Crystalline and molecular structure visualization program for materials science and computational chemistry. | http://www.xcrysden.org/ | GPL | 1.6.2 |
| XZ Utils | Compression utilities and libraries implementing the .xz file format and LZMA compression algorithms. | https://tukaani.org/xz/ | Public Domain / LGPL components | 5.2.2 |
Software Installation Policy
What can be installed in the HPC environment?
Minimum requirements for software to work in the HPC environment:
- Must run under modern Linux operating systems
- Must be properly licensed for your use
- Licensed software may be installed in the software repository; such packages must be accessible only to the research group holding the appropriate license.
- Even if the software license is free, any registration or acceptance of a license agreement must be completed by the faculty member leading the research group. HPC staff are not authorized to perform this on their behalf.
- Must work on the CPU microarchitectures currently supported by the HPC system
- Applications must be supported and actively maintained with security releases (at a minimum) by the developer
Installing Software Applications
User Installations
- Most software should be installed in a research group's project directory, a user's home directory, or used within a container environment whenever possible.
- CONDA Virtual Environment
- Build Singularity Containers from Dockerhub
Requesting the Installation of Software
- Users may request software installation through the Request Form: Cypress HPC Software Installation - Tulane IT Portal if the installation proves challenging for users.
Note:
See TracWiki
for help on using the wiki.
