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 Programing Environment
| name | description | URL | license | installed version(As of Nov 2024) | latest version(As of Nov 2024)
|
|---|
| 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, R2023a | R2024b
|
| R | software environment for statistical computing and graphics | https://www.r-project.org/ | Public | 3.1.2, 3.5.2, 3.6.1, 4.1.0, 4.1.1, 4.3.2 | 4.4.2
|
| Anaconda | distribution of the Python and R programming languages for scientific computing | https://www.anaconda.com/ | free | 2.1.0, 2.5.0, 4.0.0, 5.1.0, 2018.12, 2019.03, 2020.07, 2023.07 | 2024.2.1
|
| 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 | 18
|
| SAS | statistical software suite | https://www.sas.com/ | Commercial (site license) | 9.4 | 9.4
|
| 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. 4.8.2, 4.9.4, 6.3.0, 8.5.0, 9.5.0 | 14.2
|
| 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, 2016, 2019-update1 | software rebranded to oneAPI toolkits.
|
| name | description | URL | license | installed version(As of Nov 2024) | latest version(As of Nov 2024)
|
|---|
| Angsd | analyzing NGS data | https://www.popgen.dk/angsd/index.php/ANGSD | Public | 0.941 | 0.941
|
| Samtools | a suite of programs for interacting with high-throughput sequencing data | https://www.htslib.org/ | public | 0.1.17, 0.1.19, 1.5, 1.10, 1.13, 1.16.1 | 1.21
|
| Bcftools | programs for interacting with high-throughput sequencing data | https://samtools.github.io/bcftools/ | public | 1.16 | 1.21
|
| 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
|
| 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 | 2.2
|
| Bedops | fast, highly scalable and easily-parallelizable genome analysis toolkit | https://github.com/bedops/bedops | GPL-2 | 2.4.41 | 2.4.41
|
| Bedtools2 | a powerful toolset for genome arithmetic. | https://bedtools.readthedocs.io/en/latest/ | MIT | 2.27.1, 2.30.0 | 2.31.1
|
| 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 | 2.5.4
|
| 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 | 0.7.18
|
| 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 |
|
| 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 | 2.2.0
|
| Gatk | Genome Analysis Toolkit | https://gatk.broadinstitute.org/hc/en-us | public | 4.1.8.1, 4.5.0.0 | 4.6.0.0
|
| 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 | 2.3
|
| 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 | 2.16.0+
|
| Rsem | RNA-Seq by Expectation-Maximization | https://deweylab.github.io/RSEM/ | GPL | 1.2.31 | 1.3.3
|
| 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 | 2.68
|
| 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 | 4.0.1
|
| star | Spliced Transcripts Alignment to a Reference | https://github.com/alexdobin/STAR | MIT | 2.3.0e, 2.5.2a, 2.7.11b | 2.7.11b
|
| 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/ | 2023.2 | 2024.1
|
Computational Chemistry and Physics
| name | description | URL | license | installed version(As of Nov 2024) | latest version(As of Nov 2024)
|
|---|
| ROOT | high-energy physics tools | https://root.cern | LGPL v2.1+ | 5.34.36 | 6.32.06
|
| 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) | 09, 16 | 16
|
| 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 | 3.0.1
|
| Gromacs | molecular dynamics package designed for simulations of proteins, lipids, and nucleic acids. | https://www.gromacs.org/ | public | 5.1.2, 2016.3, 2020.7, 2021.4 | 2026.0
|
| 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 | 2Aug2023 | 29-Aug-24
|
| Rosetta | a software suite of algorithms for computational modeling and analysis of protein structures. | https://rosettacommons.org/software/ | Non-Commercial License | 3.9, 3.14 | 3.14
|
| 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 | 2.10.90
|
| name | description | URL | license | installed version(As of Nov 2024) | latest version(As of Nov 2024)
|
|---|
| OpenBLAS | Optimized BLAS (Basic Linear Algebra Subroutine) library | https://www.openblas.net/ | BSD | 0.3.18 | 0.3.28
|
| Armadillo | C++ library for linear algebra & scientific computing | https://arma.sourceforge.net/ | Apache License 2.0 | 12.6.6 | 14.0.3
|
| Atlas | Automatically Tuned Linear Algebra Software | https://math-atlas.sourceforge.net/ | BSD | 3.10.2 | 3.10.3
|
| Fftw | FFTW is a C subroutine library for computing the discrete Fourier transform (DFT). | https://www.fftw.org/ | GPL | 3.3.3, 3.3.4 | 3.3.10
|
| 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 | 1.6.10, 1.8.12, 1.8.14, 1.0.5 | 1.14.5
|
| Binutils | collection of binary tools | https://www.gnu.org/software/binutils/ | GPL | 2.37 | 2.43
|
| blcr | Berkeley Lab Checkpoint/Restart | https://crd.lbl.gov/divisions/amcr/computer-science-amcr/class/research/past-projects/BLCR/ | public | 0.8.5 | 0.8.5
|
| Boost | C++ source libraries | https://www.boost.org/ | Boost Software License | 1.57.0, 1.76.0 | 1.86.0
|
| Cmake | build system generator | https://cmake.org/ | open-source | 3.0.2, 3.12.1, 3.24.1 | 3.30.5
|
| Openmpi | MPI library | https://www.open-mpi.org/ | BSD | 4.1.6, 5.0.5 | 5.0.5
|
| 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 | 3.24.0
|
| 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 | 3.4.0
|
| 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 | 4.3.2
|
| 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 | 4.9.2
|
| GSL | The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. | https://www.gnu.org/software/gsl/ | GPL | 2.6 | 2.8
|
Other
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
Requesting the Installation of Software
