= Available Software =
[[cypress/ModuleCommand|'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)||R2013b, R2015a, R2015b, R2016a, R2017b, R2020a, R2022b, R2023a||R2024b||
||R||software environment for statistical computing and graphics||https://www.r-project.org/||Public||3.1.2, 3.2.5, 3.3.1, 3.4.1, 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))||14, 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||
||ruby||A dynamic, open-source programming language with a focus on simplicity and productivity.||https://www.ruby-lang.org/en/||BSD||2.2.3, 2.5.1||3.3.5||
||Julia||Julia is a high-level, general-purpose dynamic programming language, still designed to be fast and productive, for e.g. data science, artificial intelligence, machine learning, modeling, and simulation, most used for numerical analysis and computational science.||https://julialang.org/||MIT||1.5.2||1.11.1||
||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.||

== Bioinformatics Tools ==
||= name =||= description =||= URL =||= license =||= installed version(As of Nov 2024) =||= latest version(As of Nov 2024) =||
||Ancestry_HMM||program designed to infer adaptive introgression from population genomic data||https://github.com/russcd/Ancestry_HMM||GPL-3.0||1.0.2||1.0.2||
||Angsd||analyzing NGS data||https://www.popgen.dk/angsd/index.php/ANGSD||Public||0.941||0.941||
||bam-readcount||count DNA sequence reads in BAM files||https://github.com/genome/bam-readcount||MIT||1.0.0||1.0.1||
||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||2.17.1, 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||
||Beagle||phasing genotypes and imputing ungenotyped markers||https://faculty.washington.edu/browning/beagle/beagle.html||GPL||5.4||5.4||
||Bgen||BGEN is a compressed binary format for typed and imputed genotype data||https://enkre.net/cgi-bin/code/bgen/dir?ci\=trunk||Boost Software License v1.0, BSD||1.1.7||1.1.7||
||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, 2.3.3, 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||1.1.0, 2.1.0, 3.0.1, 3.1.0, 5.1.0, 6.0.0, 7.1.0||||
||Gatk||Genome Analysis Toolkit||https://gatk.broadinstitute.org/hc/en-us||public||4.0.4.0, 4.1.8.1, 4.5.0.0||4.6.0.0||
||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||2.5.0+, 2.10.0+, 2.12.0+||2.16.0+||
||regenie||whole genome regression modelling of large genome-wide association studies.||https://rgcgithub.github.io/regenie/||MIT||2.2.4, 3.2.7||3.6||
||Rsem||RNA-Seq by Expectation-Maximization||https://deweylab.github.io/RSEM/||GPL||1.2.19, 1.2.22, 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||1.41, 2.2||2.68||
||star||Spliced Transcripts Alignment to a Reference||https://github.com/alexdobin/STAR||MIT||2.3.0e, 2.4.0i, 2.4,2a, 2.5.2a, 2.7.19a, 2.7.11b||2.7.11b||
||Trinity||assembles transcript sequences from Illumina RNA-Seq data||https://github.com/trinityrnaseq/trinityrnaseq/releases||BSD-3||2012-06-08, 2.4.0, 2.9.5||2.15.2||
||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/||||2018.2, 2018.11, 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||
||Berkeleygw||code that calculates the quasiparticle properties and optical responses of materials||https://berkeleygw.org/||BSD||1.1-beta2||4||
||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||2016.3, 2020.7||2024.3||
||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||17Nov2016, 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||
||Comsol||COMSOL Multiphysics is a finite element analyzer, solver, and simulation software package for various physics and engineering applications, especially coupled phenomena and multiphysics.||https://www.comsol.com/||commercial (Dr. Escarra lab)||5.2, 5.3, 5.3a, 5.4, 5.6, 6.0, 6.1, 6.2 ||6.2||

== Developers Tools and Libraries ==
||= 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||2.1.5, 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||1.8.4, 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/||||3.2.4||3.4.0||||
||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 ==
||= name =||= description =||= URL =||= license =||= installed version(As of Nov 2024) =||= latest version(As of Nov 2024) =||
||Awscli||AWS Command Line Interface||https://aws.amazon.com/cli/||Public||1.29.1||1.35.11||
||Bbcp||Securely and quickly copy data from source to target||https://www.slac.stanford.edu/~abh/bbcp/||GPL||15.02.03.01.1||15.02.03.01.1||
||Cadaver||command-line WebDAV client for Unix||https://notroj.github.io/cadaver/||GPL-2||0.23.3||0.24||
||Singularity||Apptainer (formerly Singularity) simplifies the creation and execution of containers, ensuring software components are encapsulated for portability and reproducibility.||https://apptainer.org/||public||singularity/3.9.0||apptainer/1.3.4||
||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||3.1.1||
||Rclone||Rclone is a command-line program to manage files on cloud storage such as Box||https://rclone.org/||MIT||1.49.3||1.68.1||
||Gnuparallel||command-line utility allows the user to execute shell scripts or commands in parallel.||https://www.gnu.org/software/parallel/||GPL||20180322, 20230122||20241022||
||Globus Connect Personal||Create a Globus collection Create a Globus collection .||https://www.globus.org/globus-connect-personal/||public||||||


----

= 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.
* [https://wiki.hpc.tulane.edu/trac/wiki/cypress/conda_virtual_environment CONDA Virtual Environment]
* [https://wiki.hpc.tulane.edu/trac/wiki/cypress/SingularityDockerhub Build Singularity Containers from Dockerhub]

=== Requesting the Installation of Software ===
* Users may request software installation through the Request Form: [https://tulane.service-now.com/now/nav/ui/classic/params/target/com.glideapp.servicecatalog_category_view.do%3Fv%3D1%26sysparm_parent%3D8d648d93dbc44c10f460562bdc9619ad%26sysparm_catalog%3De0d08b13c3330100c8b837659bba8fb4%26sysparm_catalog_view%3Dcatalog_default%26sysparm_view%3Dcatalog_default Cypress HPC Software Installation] - Tulane IT Portal if the installation proves challenging for users.