CHPC software module catalog
A list of software that has been compiled and tested by scientific computing professionals at CHPC and is readily available on CHPC compute systems. See our modules documentation for more information.
Last updated: 14 hours ago
Pre-installed modules
| Name | Description | All versions/builds |
|---|---|---|
| 3dslicer | To run the program, run "Slicer &" in a terminal that allows X11 forwarding. If in doubt, please use FastX. |
1 versions
|
| abaqus | This module sets the environment necessary to use abaqus 2021 |
7 versions
|
| abctoolbox | This module loads the PATH environment variable for ABCtoolbox version 2009.06. |
1 versions
|
| abinit | Module which loads the environment for ABINIT (8.10.3) Abinit was compiled with: a. intel/2018.1.163 b. impi/2018.1.163 with support of MKL's BLAS, LAPACK & FFT The following additional packages/libraries can be called from ABINIT 8.10.3 a.BigDFT -> use wavelets as basis b.libXC -> library of exchange-correlation functionals c.atompaw -> Projectors Augmented Wave Functions to generate atom-centered basis functions d.wannierf90 -> Generate Maximally localised Wannier functions |
6 versions
|
| abyss | This module sets the environment necessary to use abyss version 2.1.2. |
5 versions
|
| acli |
1 versions
|
|
| adios2 | The Adaptable Input Output System version 2, developed in the Exascale Computing Program |
2 versions
|
| admixture |
1 versions
|
|
| advisor | This module sets the variables for Intel Advisor XE |
1 versions
|
| agat | This module sets up the environment for the AGAT anaconda environment version 0.9.2. |
1 versions
|
| alamode | ALAMODE, installed with conda |
1 versions
|
| alder | ALDER: Admixture-induced Linkage Disequilibrium for Evolutionary Relationships Binary: alder |
1 versions
|
| almabte | almaBTE is a software package that solves the space- and time-dependent Boltzmann transport equation for phonons, using only ab-initio calculated quantities as inputs |
1 versions
|
| alphafold | To start Alphafold, run "run_alphafold.sh" To see Alphafold runtime options, run "run_alphafold.sh --help" The database paths are in the AFDATA environment variable and are already included in the run_alphafold.sh command For license requirements, detailed documentation and important performance aspects see https://www.chpc.utah.edu/documentation/software/alphafold.php#alphafold3 |
8 versions
|
| alphapulldown | Any help you want to display when running "module help module-name" |
1 versions
|
| amanzi | Amanzi, the Multi-Process HPC Simulator is a highly modular and extensible computational engine for simulations of flow and reactive transport. It is capable of simulating transient saturated and variably saturated (Richards) flows, transport with non-grid-aligned dispersion and a variety of reactions. In the future it will include non- isothermal, multi-phase multi-component, geo-mechanical, and surface water models. To achive this ambitious goal we are building Amanzi as a grass-roots collaboration of an emerging broader community of geoscienists, computational and computer scientists, and applied mathematicians. This broader community is leveraging its extensive experience, existing capabilities, and untapped advances from their areas of expertise to develop Amanzi. |
2 versions
|
| amber | Amber is a suite of biomolecular simulation programs together with Amber tools. Note: The version number is composed of the Amber version (major) and the tools version (minor). A manual download is required for both Amber and Amber tools. Spack will search your current directory for the download files. Alternatively, add the files to a mirror so that Spack can find them. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html |
33 versions
|
| amd-libm | AMD Math Library (LibM) AMD LibM is a software library containing a collection of basic math functions optimized for x86-64 processor based machines. It provides many routines from the list of standard C99 math functions. NOTE: a.This library was GCC compiled. b.For vector routines, use amdlibm_vec.h in your C/C++ code. c.Make sure tht -lalm precede -lm d. Compilation: gcc -I$INCDIR Linking: either :: -L$LIBDIR -lalm -lm or :: -Wl,-rpath=$LIBDIR -L$LIBDIR -lalm -lm |
1 versions
|
| amos | This module loads the anaconda environment for amos version 3.1.0 |
1 versions
|
| ampliconarchitect | AmpliconArchitect v.1.3.r1 The following environmental variables have been set for AmpliconArchitect a. AA_DATA_REPO :: /uufs/chpc.utah.edu/sys/installdir/r8/ampliconarchitect/1.3.r1/data_repo b. AA_SRC :: /uufs/chpc.utah.edu/sys/installdir/r8/ampliconarchitect/1.3.r1/src c. AA :: "python3 /uufs/chpc.utah.edu/sys/installdir/r8/ampliconarchitect/1.3.r1/src/AmpliconArchitect.py" Note that you can overwrite the env. variable AA_DATA_REPO by your own repository! |
1 versions
|
| ampliconclassifier | AmpliconClassifier v. 0.4.11 The following environmental variables have been set for AmpliconArchitect a. AA_DATA_REPO :: /uufs/chpc.utah.edu/sys/installdir/r8/ampliconarchitect/1.3.r1/data_repo b. AC_SRC :: /uufs/chpc.utah.edu/sys/installdir/r8/ampliconclassifier/0.4.11 Note that you can overwrite the env. variable AA_DATA_REPO by your own repository! |
1 versions
|
| anaconda | This module sets the PATH variable for anaconda3/2019.07 (i.e. python/2.7.16) |
2 versions
|
| anaconda3 | This module sets the PATH variable for anaconda3/2023.03 |
9 versions
|
| angsd | ANGSD is a software for analyzing next generation sequencing data Executable: angsd |
3 versions
|
| annovar | This module sets the environment necessary to use annovar |
1 versions
|
| ansys | This module sets the environment to run Ansys version 21.2 |
11 versions
|
| ansysedt | This module sets the environment necessary to use Ansys EDT 21.2 |
5 versions
|
| antismash | This module sets the dependencies for antismash After LOADING the antismash module, each USER of antismash has to do the following: A.Perform ONCE: (local installation) ------------ export NOW=`date +"%m%d%Y"` export DIR=$HOME/AS mkdir -p $DIR # Clone the latest version of antismash cd $DIR git clone https://bitbucket.org/antismash/antismash.git $NOW # Download the databases cd $DIR/$NOW python download_databases.py B.Set the PATH to use: (path needs to be set to use antismash) ------------------- export PATH=$DIR/$NOW:$PATH |
1 versions
|
| anvio | This module sets up anvi'o container by aliasing the container shell login to the runanvi command Based on DockerHub container https://hub.docker.com/r/meren/anvio Run as "runanvi arguments". |
1 versions
|
| aocc | The AOCC compiler system is a high performance, production quality code generation tool. The AOCC environment provides various options to developers when building and optimizing C, C++, and Fortran applications targeting 32-bit and 64-bit Linux platforms. The AOCC compiler system offers a high level of advanced optimizations, multi-threading and processor support that includes global optimization, vectorization, inter-procedural analyses, loop transformations, and code generation. AMD also provides highly optimized libraries, which extract the optimal performance from each x86 processor core when utilized. The AOCC Compiler Suite simplifies and accelerates development and tuning for x86 applications. Please install only if you agree to terms and conditions depicted under : http://developer.amd.com/wordpress/media/files/AOCC_EULA.pdf Example for installation: 'spack install aocc +license-agreed' |
4 versions
|
| apache-ant | This module provides the environment necessary to use Apache Ant |
1 versions
|
| apbs | This module sets the environment necessary to use APBS, version1.5 |
1 versions
|
| apptainer | This module sets up Apptainer, a successor to Singularity. |
10 versions
|
| aretomo | This module loads the PATH environment variable for AreTomo version 1.3.4. |
2 versions
|
| aretomo2 | This module loads the PATH environment variable for AreTomo2 version 1.1.2. |
1 versions
|
| aretomo3 | This module loads the PATH environment variable for AreTomo3 version 2.0.3. |
1 versions
|
| argweaver | This module loads the PATH and PYTHONPATH environment variables for argweaver released on 2020-03-06. |
1 versions
|
| aria2 | This module provides the environment necessary to run aria2, a data transfer tool. To see options for use: aria2c -h |
1 versions
|
| armadillo | Armadillo is a high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use. |
3 versions
|
| arpack-ng | ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. Important Features: * Reverse Communication Interface. * Single and Double Precision Real Arithmetic Versions for Symmetric, Non-symmetric, Standard or Generalized Problems. * Single and Double Precision Complex Arithmetic Versions for Standard or Generalized Problems. * Routines for Banded Matrices - Standard or Generalized Problems. * Routines for The Singular Value Decomposition. * Example driver routines that may be used as templates to implement numerous Shift-Invert strategies for all problem types, data types and precision. This project is a joint project between Debian, Octave and Scilab in order to provide a common and maintained version of arpack. Indeed, no single release has been published by Rice university for the last few years and since many software (Octave, Scilab, R, Matlab...) forked it and implemented their own modifications, arpack-ng aims to tackle this by providing a common repository and maintained versions. arpack-ng is replacing arpack almost everywhere. |
6 versions
|
| arpip | ARPIP: Ancestral sequence Reconstruction under Poisson Indel Process |
1 versions
|
| arrow | The Arrow C++ library. Language-independent columnar memory format for flat and hierarchical data, organized for efficient analytic operations on modern hardware like CPUs and GPUs. |
1 versions
|
| asciidoc | This module sets the PATH for Asciidoc 8.6.9 |
1 versions
|
| asfdaac | This module sets the PATH environment variable for the asfdaac module, version 1.0. |
1 versions
|
| aspera | IBM Aspera is a suite of data transfer software for moving amounts of data quickly and securely, regardless of network conditions. |
2 versions
|
| atacgraph | Module which sets the PATH variable for ATACgraph. |
1 versions
|
| ataqv | run: ataqv --help |
1 versions
|
| atmos_env | This module sets up the environment for the atmos_env anaconda environment version 1.0. This is still experimental! Use at your peril! |
2 versions
|
| atsas | Any help you want to display when running "module help module-name" |
1 versions
|
| augustus | This module sets the environment necessary to use augustus, version 3.5.0 |
3 versions
|
| autoconf | This module loads the PATH variable for Autoconf version 2.69 |
1 versions
|
| autodock | This module provides the environment necessary for AutoDock 4.2.6 |
2 versions
|
| autodock-gpu | This module sets the environment necessary to use GPU-enabled version of autodock 1.5.2. |
1 versions
|
| autodock-vina | This module provides the environment necessary for AutoDock-Vina 1.2.5 AutoDock Vina is one of the fastest and most widely used open-source docking engines. Name of the executables: vina, vina_split |
2 versions
|
| automake | Automake -- make file builder part of autotools |
2 versions
|
| autometa |
1 versions
|
|
| aws-cli | This module loads the PATH environment variable for aws-cli version 2.2.29. |
1 versions
|
| bali-phy | This module sets the environment to run Bali-Phy version 3.5.0. |
2 versions
|
| bamliquidator | This module sets up bamliquidator container by aliasing the container run to the bamliquidator command Run as "bamliquidator arguments". |
1 versions
|
| bamquery | Any help you want to display when running "module help module-name" |
1 versions
|
| bamtools | This module sets the environment necessary to use bamtools 2.5.2 |
2 versions
|
| basic | This module sets up the environment for the BASIC package. |
1 versions
|
| bayestraits | This package loads the environment to run bayestraits version 3.0.2 |
1 versions
|
| baypass | This module provides the environment necessary to run baypass from https://forge.inrae.fr/mathieu.gautier/baypass_public#get-baypass |
1 versions
|
| bazel | Module to set the env. variables for Bazel (Version 0.5.1) |
3 versions
|
| bbftp | This module sets the path for bbftp |
1 versions
|
| bbtools | BBTools is a suite of bioinformatics tools for analysis of DNA and RNA sequencing data |
1 versions
|
| bcftools | This package loads the environment to run bcftools, To run bcftools load module and run 'bcftools' |
7 versions
|
| bcl2fastq2 | This package loads the environment to run bcl2fastq version 2.20 Type bcl2fastq -h to see options |
2 versions
|
| beagle | This module provides the environment necessary to run java code beagle, version 5.4. To run do $beagle to see formata. |
4 versions
|
| bear | Bear is a tool that generates a compilation database for clang tooling from non-cmake build systems. |
1 versions
|
| beast | This module loads the PATH environment variable |
4 versions
|
| bedops | BEDOPS: high-performance genomic feature operations |
1 versions
|
| bedtools | Module which sets the PATH variable for bedtools. |
2 versions
|
| berkeleygw | BerkeleyGW is a many-body perturbation theory code for excited states, using the GW method and the GW plus Bethe-Salpeter equation (GW-BSE) method to solve respectively for quasiparticle excitations and optical properties of materials. |
2 versions
|
| binutils | GNU binutils, which contain the linker, assembler, objdump and others |
3 versions
|
| bioawk | This module loads the PATH environment variable for bioawk version 1.0. |
1 versions
|
| biobakery | This module sets up bioBakery container by aliasing the container shell login to the bioBakery command Based on DockerHub container https://hub.docker.com/r/biobakery/workflows Run as "runbioBakery arguments". |
3 versions
|
| biokevlar | Biokevlar Testbed for developing reference-free variant discovery methods for genomics. |
1 versions
|
| biolib | Module which sets the PATH variable for user instaled miniforge To check the available packages: conda list |
1 versions
|
| biom | This module loads the PATH and PYTHONPATH environment variables for biom version 2.1.16. |
1 versions
|
| bioperl | Loads the bioperl scripts into the environment. This module requires the perl module load to be loaded. To see a list of scripts navigate to the following directory: /uufs/chpc.utah.edu/sys/pkg/bioperl/1.5.1/bin |
1 versions
|
| bismark | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
2 versions
|
| blast | NCBI Blast for sequence alignment, version 2.11.0. As of 6/28/2019 the Blast programs are using database files located in one of several /scratch file system locations, depending on which cluster you use: Cluster Database file location redwood /scratch/general/pe-nfs1/app-repo/blastdb/DbFiles/v5 kingspeak /scratch/general/vast/app-repo/blastdb/DbFiles/v5 notchpeak /scratch/general/vast/app-repo/blastdb/DbFiles/v5 ember /scratch/general/nfs1/app-repo/blastdb/DbFiles/v5 lonepeak /scratch/general/nfs1/app-repo/blastdb/DbFiles/v5 These database files are updated on the 4th of each month. |
3 versions
|
| blat | This module sets up the environment for blat version 36x5 |
1 versions
|
| boldigger3 | boldigger3 --help |
2 versions
|
| boltz1 | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
1 versions
|
| boltz2 | Module which sets the PATH variable for Boltz2 (Python venv) To check help page: boltz --help |
3 versions
|
| boltzgen | BoltzGen: Toward Universal Binder Design |
1 versions
|
| bonito | This module loads the PATH and other environment variables for bonito version 0.5.0 for GPU execution. |
1 versions
|
| boost | Boost provides free peer-reviewed portable C++ source libraries, emphasizing libraries that work well with the C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications. The Boost license encourages both commercial and non-commercial use. |
31 versions
|
| bowtie | Bowtie is a genomics aligner for short DNA sequences. More info can be found here: http://bowtie-bio.sourceforge.net/index.shtml Run using "bowtie". |
1 versions
|
| bowtie2 | Bowtie is a genomics aligner for short DNA sequences. More info can be found here: http://bowtie-bio.sourceforge.net/index.shtml Run using "bowtie2. |
1 versions
|
| bpp | BPP is a Bayesian Markov chain Monte Carlo (MCMC) program for analyzing sequence alignments from multiple loci and multiple closely-related species under the multispecies coalescent (MSC) model. |
1 versions
|
| bpp-core | Bio++ core library. |
1 versions
|
| bpp-phyl | Bio++ phylogeny library. |
1 versions
|
| bpp-phyl-omics | Bio++ Phylogenetic Omics Library |
1 versions
|
| bpp-seq | Bio++ seq library. |
1 versions
|
| bpp-seq-omics | Bio++ Sequence Omics Library |
1 versions
|
| bracken | This module sets the environment for bracken version 2.5. |
2 versions
|
| braker | Any help you want to display when running "module help module-name" |
5 versions
|
| bridger | Bridger : An Efficient De novo Transcriptome Assembler For RNA-Seq Data |
1 versions
|
| bsoft | Provides access to "Bernard's Software Package", tools focused on protein structure analysis and prediction. |
4 versions
|
| btop | This module provides the environment necessary to run btop, an interactive system & process monitor tool. To see options for use: btop -h |
1 versions
|
| busco | This module sets up the environment to run busco version 5.3.2 from https://hub.docker.com/r/ezlabgva/busco:v5.3.2_cv1 by aliasing the container call to the busco executable. |
2 versions
|
| bwa | This module sets the PATH variable for bwa Executable: bwa |
2 versions
|
| bwa-mem | This module sets the PATH variable for bwa-mem. Run as bwa-mem2 |
1 versions
|
| c01classifier | This module loads the PATH environment variable for C01Classifier version 5.1.0. |
1 versions
|
| cactus | Module to load cactus, a genome aligner based upon notion of Cactus graphs (CPU version requires AVX2) |
4 versions
|
| cafe | This module sets up the environment for CAFE, version 4.2.1. |
1 versions
|
| caffe | Caffe 1.0.0 container running Ubuntu 18.04. Defines the following commands: - "caffe" - Caffe executable - "python3" - iner which includes Caffe and all its depenencies |
1 versions
|
| caffe2 | Caffe2 0.8.1 container running Ubuntu 16.04. Defines the following commands: - "python" - which includes Caffe2 and all its depenencies |
1 versions
|
| caiman | CaImAn |
1 versions
|
| cairo | Cairo is a 2D graphics library with support for multiple output devices. |
1 versions
|
| cameratraps | single image: python $CAMERATRAPS_BASE/CameraTraps/detection/run_detector.py $CAMERATRAPS_BASE/md_v5a.0.0.pt --image_file "cat.jpg" batch processing: python $CAMERATRAPS_BASE/CameraTraps/detection/run_detector_batch.py $CAMERATRAPS_BASE/md_v5a.0.0.pt $HOME/images $HOME/images_out.json |
1 versions
|
| cantera | Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes. |
10 versions
|
| cantera-pokitt | Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes. |
2 versions
|
| canu | Canu is a single molecule sequence assembler for genomes |
3 versions
|
| cap3 | This module sets the PATH environment variables for cap3 version 3.0. |
1 versions
|
| carpy | This module loads the Environmentable Variables for CarPy (v. 2013-06-17) |
1 versions
|
| casa | CASA: Common Astronomy Software Applications (General Use) # Based on Python/3.12 |
3 versions
|
| casa-alma | CASA: Common Astronomy Software Applications (ALMA Pipeline) |
1 versions
|
| casa-vla | CASA: Common Astronomy Software Applications (VLA Pipeline) |
1 versions
|
| catch2 | Catch2 is a multi-paradigm test framework for C++, which also supports Objective-C (and maybe C). |
2 versions
|
| cbc | Cbc (Coin-or branch and cut) is an open-source mixed integer programming solver written in C++. It can be used as a callable library or using a stand-alone executable. The following env. variables are set/modified: PATH /uufs/chpc.utah.edu/sys/installdir/cbc/2.9.7/bin:$PATH CBC_DIR /uufs/chpc.utah.edu/sys/installdir/cbc/2.9.7 CBC_INCDIR /uufs/chpc.utah.edu/sys/installdir/cbc/2.9.7/include CBC_LIBDIR /uufs/chpc.utah.edu/sys/installdir/cbc/2.9.7/lib |
1 versions
|
| ccache | ccache is a compiler cache. It speeds up recompilation by caching previous compilations and detecting when the same compilation is being done again. |
1 versions
|
| ccl | This module loads the Intel Collective Communications Library |
1 versions
|
| ccp4 | This module loads the environment for ccp4 |
2 versions
|
| ccpem | CCP-EM (Nightly build) 11 Nov. 2021 depends on: modeller (executable: mod9.20) ccp4/7.1.016 AND python (in /bin/python) |
2 versions
|
| cctools | Module which loads the cctools environment. It contains: a. Parrot : Parrot Virtual File System b. Chirp : Chirp Distributed File System c. Makeflow : Workflow System d, Wirk Queue: A Scalable Master/Worker Framework e. SAND : Scalable Assembly @ Notre Dame f. etc.. |
1 versions
|
| cdbfasta | This module loads the PATH environment variable for cdbfasta version 1.0. |
1 versions
|
| cdo | CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. |
9 versions
|
| cellbender | This module sets up the environment for the Cellbender package from the Broad Institute. To cite, please visit this page: https://github.com/broadinstitute/CellBender#citing-cellbender. |
1 versions
|
| cellprofiler | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
1 versions
|
| cellranger | Cell Ranger is a package from 10X Genomics for single-cell sequence analysis. More information can be found here: https://support.10xgenomics.com/ This module loads the environment for Cellranger version 9.0.1 The reference data are to be found in: /uufs/chpc.utah.edu/sys/installdir/cellranger/refdata-gex-GRCh38-2020-A |
7 versions
|
| cellranger-arc | Cell Ranger ARC is a package from 10X Genomics for single-cell sequence analysis. More information can be found here: https://support.10xgenomics.com/ This module loads the environment for Cellranger ARC version 2.0.2. The reference data are to be found in: /uufs/chpc.utah.edu/sys/installdir/cellranger/refdata-gex-GRCh38-2020-A |
1 versions
|
| cereal | cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone. |
1 versions
|
| cfdem | This module loads CFDEM coupling (3.8.0) and dependencies (openmpi/4.1.4 and vtk/7.1.0); Compiled executables: cfdemPostproc, cfdemSolverIB, cfdemSolverPiso, cfdemSolverPisoScalar, cfdemSolverPisoSTM Repos and commits used: 1) CFDEM coupling 3.8.0 https://github.com/CFDEMproject/CFDEMcoupling-PUBLIC.git commit b23726463721d5d83c419b8c0b612950e6c4c7c8 2) LIGGGHTS https://github.com/CFDEMproject/LIGGGHTS-PUBLIC.git commit 9fb7f67592be9304afca9cb6840892b3b7d048d6 3) lpp https://github.com/CFDEMproject/LPP.git commit 633058e1abb8b9bea1f9e6e47ceae8376ad3661a 4) OpenFOAM 5.x https://github.com/OpenFOAM/OpenFOAM-5.x.git commit 7f7d351b741bf6406366a043cac98de56d2d44dd 5) OpenFOAM-ThirdParty 5.x https://github.com/OpenFOAM/ThirdParty-5.x.git commit a807587a7babd4d03b62794b26e5ef4105301416 |
2 versions
|
| cfitsio | CFITSIO: Library of C and Fortran subroutines for reading & writing data files in FITS (Flexible Image Transport System) Env. Variables: CFITSIO_INCDIR CFITSIO_LIBDIR (libcfitsio.a) |
4 versions
|
| cfm | CFM-ID Competitive Fragmentation Modeling for Metabolite Identification |
2 versions
|
| cget | cget: C++ package retrieval |
1 versions
|
| charliecloud | Lightweight user-defined software stacks for HPC. |
4 versions
|
| charmm | Module file for charmm 46b2 free version, built with gcc/8.5.0 and openmpi/4.1.3 |
2 versions
|
| chemem | Module which sets the PATH variable for ChemEM which is built on top of python/3.11 Executable: chemem |
3 versions
|
| chimera | This module provides the environment necessary for Chimera 1.17.3 |
1 versions
|
| chimerax | This module provides the environment necessary for Chimera 1.7.1 Name of the executable: chimerax |
4 versions
|
| chpc | CHPC Modules |
1 versions
|
| chpcscripts | This module provides access to CHPC specific scripts and tool that may assist users with launching jobs and other tasks. |
1 versions
|
| ciao | Chandra Interactive Analysis of Observations (CIAO) |
2 versions
|
| circos | This module provides the environment necessary to run java code Corcos, verrion 0.69-5. To run do circos, add --help to see options. |
1 versions
|
| cistem | to use -- ml cistem cisTEM & starts gui |
2 versions
|
| clean | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
1 versions
|
| cloudy | This loads the Cloudy module |
2 versions
|
| cmake | CMAKE - Version 3.26.0 Executables:: cmake ccmake cmake-gui cpack ctest |
7 versions
|
| cmg | This module loads environment variables for CGM version 2023.119.GU (2023.41 Release). |
1 versions
|
| cnvnator | This package loads the environment for htslib. |
1 versions
|
| code-server | code-server is VS Code running on a remote server, accessible through the browser. |
1 versions
|
| codeblocks | Module which loads the env. variables for Code::Blocks Executables: codeblocks cb_console_runner cb_share_config |
2 versions
|
| colab | Any help you want to display when running "module help module-name" |
2 versions
|
| colabfold | This package loads environment for Colabfold local execution To start the program, use 'colabfold_batch' at the command line. Run 'colabfold_batch --help' for options |
6 versions
|
| comsol | This module loads the Comsol 5.5 environment |
2 versions
|
| conga | This module sets up the environment for the Conga package. |
1 versions
|
| coot | Coot is a Crystallographic Object-Oriented Toolkit for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data. |
3 versions
|
| corretto | Corretto 11:: OpenJDK version Help: java --version User Guide:: https://docs.aws.amazon.com/corretto/latest/corretto-11-ug/corretto-11-ug.pdf |
1 versions
|
| 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 |
14 versions
|
| crabs | run: crabs -h |
1 versions
|
| crest | CREST : Conformer-Rotamer Ensemble Sampling Tool Utility and Driver Tool for xtb |
1 versions
|
| crispresso | Module which sets the PATH variable for CRISPresso version 1.0.9. |
1 versions
|
| cromwell | Cromwell is a Workflow Management System geared towards scientific workflows |
1 versions
|
| cryodrgn | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
3 versions
|
| cryodrgn-ai | This module sets up the environment for the Conga package. |
1 versions
|
| cryolo | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
3 versions
|
| cryosparc-tools | cryosparc-tools :: Development version The documentation is to be found in: /uufs/chpc.utah.edu/sys/installdir/r8/cryosparc-tools/08192024/docs/_build/html/index.html |
1 versions
|
| csd | Loads the Cambridge Structural Database, v2024.3, including Mercury, ConQuest, Gold, CrossMiner and other related software in the CSD Suite. |
5 versions
|
| ctffind | This package loads the environment to run ctffind version 4.1.14. To use, there is program ctffind and script ctffind_plot_results.sh |
2 versions
|
| cubit | This module sets the environment necessary to use Cubit |
1 versions
|
| cuda | CUDA is a parallel computing platform and programming model invented by NVIDIA. It enables dramatic increases in computing performance by harnessing the power of the graphics processing unit (GPU). Note: This package does not currently install the drivers necessary to run CUDA. These will need to be installed manually. See: https://docs.nvidia.com/cuda/ for details. |
42 versions
|
| cudnn | NVIDIA cuDNN is a GPU-accelerated library of primitives for deep neural networks |
27 versions
|
| cufflinks | This package loads the environment to run cufflinks version 2.1.2 To start type 'cufflinks' at the command lina; see contents of /uufs/chpc.utah.edu/sys/installdir/cufflinks/2.2.1 for toher commands |
1 versions
|
| cupy | CuPy 12.3.0 : NumPy/SciPy compatible array library for GPU-accelerated computing with Python. |
4 versions
|
| cusparselt | cuSPARSELt : A High-Performance CUDA Library for Sparse Matrix-Matrix Multiplication (cusparseLt is supported only on GPU devices with compute capability == 8.0, 8.6, 8.9) Env. variables: CUSPARSELT_ROOTDIR :: /uufs/chpc.utah.edu/sys/installdir/r8/cusparselt/0.4.0 CUSPARSELT_INCDIR :: /uufs/chpc.utah.edu/sys/installdir/r8/cusparselt/0.4.0/include CUSPARSELT_LIBDIR :: /uufs/chpc.utah.edu/sys/installdir/r8/cusparselt/0.4.0/lib User-Guide: https://docs.nvidia.com/cuda/cusparselt/index.html Examples: https://github.com/NVIDIA/CUDALibrarySamples/tree/master/cuSPARSELt e.g. module load cuda/12.2.0 module load cusparselt nvcc -c -I$CUSPARSELT_INCDIR matmul_example.cpp nvcc -o matmul_example matmul_example.o -L$CUSPARSELT_LIBDIR -lcusparseLt -lcusparse -ldl ./matmul_example |
1 versions
|
| cutadapt | This module loads the PATH and PYTHONPATH environment variables for cutadapt version 3.5. Installed by Brett Milash |
3 versions
|
| cutensor | cuTENSOR: Tensor Linear Algebra on NVIDIA GPUs having: a.Direct tensor contractions b.Tensor reductions (including partial reductions) c.Element-wise tensor operations Env. variables: CUTENSOR_ROOTDIR :: /uufs/chpc.utah.edu/sys/installdir/r8/cutensor/1.7.0 CUTENSOR_INCDIR :: /uufs/chpc.utah.edu/sys/installdir/r8/cutensor/1.7.0/include CUTENSOR_LIBDIR :: /uufs/chpc.utah.edu/sys/installdir/r8/cutensor/1.7.0/lib/12 (CUDA 12.*) User-Guide: https://docs.nvidia.com/cuda/cutensor/user_guide.html Examples: https://github.com/NVIDIA/CUDALibrarySamples/tree/master/cuTENSOR e.g. module load cuda/12.2.0 module load cutensor/1.7.0 nvcc -c -I$CUTENSOR_INCDIR -std=c++11 contraction.cu nvcc -o contraction contraction.o -L$CUTENSOR_LIBDIR -lcutensor |
5 versions
|
| cwf | This module sets the environmental variables for COASTWATCH v. 3.3.0 |
1 versions
|
| cwutil | This loads the CoastWatch utilities. |
1 versions
|
| cyana | This module loads the environment for CYANA |
1 versions
|
| dal | This module loads the Intel Data Analytics Library |
1 versions
|
| dars | This module sets the environment necessary to use DARS 2.12.005 |
1 versions
|
| davix | High-performance file management over WebDAV/HTTP. |
1 versions
|
| ddt | This module loads the environment for the DDT debugger |
6 versions
|
| debugger | This module loads the Intel Distribution for GDB |
1 versions
|
| deepemhancer | Module which sets the PATH variable for deepEMhancer To check the available packages: conda list |
1 versions
|
| deepetpicker | DeepETPicker : A deep learning based open-source software with a friendly user interface to pick 3D particles rapidly and accurately from cryo-electron tomograms Executable: DeepETPicker |
1 versions
|
| deeplearning | This module sets up the environment to run the deeplearning environment version 2024.2.0. |
12 versions
|
| deepmd | Any help you want to display when running "module help module-name" |
1 versions
|
| deeptools | This module loads the PATH and PYTHONPATH environment variables for deepTools version 3.5.1. |
3 versions
|
| delft3dvis | Module to set the environmental variables for delft3dvis (visualization scripts) that came with delft3d (5275) and use R2009b. The executables are: d3d_qp (Quickplot) ecoplot (Ecoplot) |
1 versions
|
| delly | DELLY2: Structural variant discovery by integrated paired-end and split-read analysis |
1 versions
|
| densitree | This module loads the environment for the DensiTree program, which performs qualitative analyses of sets of trees. |
1 versions
|
| dfast | This module loads the PATH environment variable for dfast version 1.0.5. |
1 versions
|
| dhsvm | DHSVM: Distributed Hydrology Soil Vegetation Model (DHSVM) Name executable: dhsvm (alias for DHSVM3.1.1) |
1 versions
|
| diamond | Module which sets the env. variables for the diamond package diamond help |
3 versions
|
| diffuse | This module sets the environment for diffuse |
1 versions
|
| digenome-seq | This module sets the environment necessary to use digenome-seq |
1 versions
|
| digenome-toolkit2 | This module sets the environment necessary to use digenome-toolkit2 |
2 versions
|
| dirac | DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations |
1 versions
|
| discovar-denovo | This module loads the PATH environment variable for discovar-denovo version 52488. Executables available from this module include: AffineAlign CmpSeq CrossOut DiscovarDeNovo EdgeInfo FormPath MakeLookupTable NhoodInfo QueryLookupTable SeqInfo |
1 versions
|
| discus | This module sets up discus v6.14.02 built on Ubuntu 22.04 Executables: discus_suite, pgxwin_server |
1 versions
|
| dislin | This module sets the following env. variables: a. PATH b. LD_LIBRARY_PATH for the dislin libraires, version 11.2 for Centos7 |
1 versions
|
| dissolve | This module sets the env to run the dissolve serial version (dissolve) and gui (dissolve-gui). |
1 versions
|
| django | This module sets the environmental variables for Django package 1.9.7. The package relies on: python/3.5.1 anaconda3/4.0.0 postgresql 9.5.3 (/usr/pgsql-9.5/bin on Centos7) Note: The package has been compiled for CENTOS7 |
1 versions
|
| dnanexus-sdk | This module loads the DNANEXUSHOME, PATH and PYTHONPATH environment variables for the DNAnexus Platform Software Development Kit version 0.231.0. |
1 versions
|
| dnanexus-ua | This module loads the PATH environment variable for the DNAnexus Upload Agent (ua) software. |
1 versions
|
| dnnl | This module loads the Intel Deep Neural Network Library |
1 versions
|
| docbook-xml | Docbook DTD XML files. |
1 versions
|
| docbook-xsl | DocBook XSLT 1.0 Stylesheets. |
1 versions
|
| dockstore | Dockstore provides a place for users to share tools encapsulated in Docker and described with the Common Workflow Language (CWL), WDL (Workflow Description Language), Nextflow, or Galaxy. For the live site, see Dockstore.org. |
1 versions
|
| dolfinx_mpc | This sets up Dolfinx MPC in a container. Run with the "python" command. Note that this uses real numbers, complex numbers require settings changes which are not implemented in this module. |
1 versions
|
| dorado | Dorado: a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads has GPU acceleration EXECUTABLE: dorado |
4 versions
|
| doxygen | doxygen - standard tool to generate documentation from annotated C++ sources. also supports:C, C#, Java, Python, IDL, Fortran. |
3 versions
|
| dpct | This module loads the Intel DPC++ Compatibility Tool |
1 versions
|
| dpl | This module loads the Intel DPC++ Library |
1 versions
|
| dram | DRAM (Distilled and Refined Annotation of Metabolism) Note: a. Do NOT "conda activate DRAM" (totally not necessary) b. The DB are stored in: /scratch/general/lustre/app-repo/dram/databases |
1 versions
|
| dropest | This module loads the PATH and other environment variables for dropEst version 0.8.6. |
1 versions
|
| ds9 | SAOImageDS9 :: SAOImageDS9 is an astronomical imaging and data visualization application. DS9 supports FITS images and binary tables, multiple frame buffers, region manipulation, and many scale algorithms and colormaps. Executable :: ds9 |
2 versions
|
| dssp | This module sets the environment necessary to use dssp, a program which ed to calculate secondary structure information from PDB files |
2 versions
|
| duckdb | DuckDB is an in-process SQL OLAP Database Management System. |
1 versions
|
| dxtoolkit | run: dx --h; dx --version |
1 versions
|
| dynamo | This module sets the variables for Dynamo |
2 versions
|
| eautils | Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs. |
1 versions
|
| eccodes | ecCodes is a package developed by ECMWF for processing meteorological data in GRIB (1/2), BUFR (3/4) and GTS header formats. |
1 versions
|
| edem | This module sets the environment to run EDEM |
2 versions
|
| eigen | Eigen is a C++ template library for linear algebra matrices, vectors, numerical solvers, and related algorithms. |
6 versions
|
| eigensoft | This modulr sets the path for the 6.0.1 Eigensoft installation |
1 versions
|
| elasticsearch | This module sets up Elasticsearch |
1 versions
|
| elphbolt | ElPhBolt :: A solver for the coupled and decoupled electron and phonon Boltzmann transport equations. EXEs: elphbolt, screening_comparison, superconda |
1 versions
|
| emacs | This module provides the environment necessary to run emacs. To see options for use: 'man emacs' |
4 versions
|
| eman2 | This module sets the environment necessary to use EMAN2, version 2.99 |
5 versions
|
| epacts | Any help you want to display when running "module help module-name" |
1 versions
|
| esmf | The Earth System Modeling Framework (ESMF) is high-performance, flexible software infrastructure for building and coupling weather, climate, and related Earth science applications. The ESMF defines an architecture for composing complex, coupled modeling systems and includes data structures and utilities for developing individual models. |
2 versions
|
| esmfold | run: which python |
1 versions
|
| etk | This module sets up the environment for the einstein toolkit software version 2022.11. |
2 versions
|
| evidencemodeler | This module sets the environment necessary to use EVidence Modeler |
1 versions
|
| exonerate | This module sets the environment necessary to use exonerate allows for the alignment of sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics |
1 versions
|
| fasta | This module sets up the environment for fasta version 36.3.8h. |
1 versions
|
| fastcn | This module loads the PATH environment variable for fastCN (github commit 538a5d8; Jul 11,2022). |
1 versions
|
| fastml | This module sets the environment to run FastML version 3.11. |
1 versions
|
| fastp | This module loads the PATH environment variable for fastp version 0.20.1. |
1 versions
|
| fastqc | This package loads the environment to run fastqc version 0.12.1 . To start type 'fastqc' at the command line . |
2 versions
|
| fasttree | This module provides the environment necessary for fastree 1.2.9, specifically FastTreeMP, with is the openMP version |
1 versions
|
| fastx | Loads the FastX client for persistent X11 sessions. |
1 versions
|
| fastx_toolkit | This module sets the PATH for running the fastx_toolkit |
1 versions
|
| fatcat | This module sets the environment necessary to use FATCAT version 2.0. |
1 versions
|
| fbat | This module sets the environment necessary to use fbat 2.0.3 FBAT implements a broad class of Family Based Association Tests |
1 versions
|
| febio |
3 versions
|
|
| feflow | This module sets the environment necessary to use feflow, version 6.2 |
1 versions
|
| fenglab | This module sets the PATH environment variable for the fenglab installed packages |
1 versions
|
| fenics | FEniCSx project in a Singularity container |
1 versions
|
| fenics-basix | Basix is a finite element definition and tabulation runtime library |
2 versions
|
| fenics-dolfinx | Next generation FEniCS problem solving environment |
4 versions
|
| fenicsx | This module loads the PATH and PYTHONPATH environment variables for FEniCSx version 0.9. |
1 versions
|
| ferret | This module loads the Ferret environment |
1 versions
|
| ffmpeg | FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video. |
9 versions
|
| fftw | FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for most applications. |
27 versions
|
| fhi-aims | FHI-aims: All-electron electronic structure theory with numeric atom-centered orbitals |
1 versions
|
| fiji | This module sets the environment necessary to use Fiji. ImageJ-linux64 # start GUI |
2 versions
|
| findbugs | This module sets the variables for Findbugs 1.3.9 |
1 versions
|
| findem | This module sets the environment necessary to use FindEM v2 series of programs to help with automated particle picking from electron micrographs |
1 versions
|
| fish | This module loads the fish 3.1.0 shell |
1 versions
|
| fishr2 | This module sets the environment to run FISHR2 version Feb28_2018. |
1 versions
|
| fithichip | This module loads the PATH and other environment variables for fithichip version 9.1. |
1 versions
|
| fitsverify | This module sets the environmental variables for fitsverify (v.4.17) |
1 versions
|
| fltk | FLTK (pronounced "fulltick") is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation. FLTK is designed to be small and modular enough to be statically linked, but works fine as a shared library. FLTK also includes an excellent UI builder called FLUID that can be used to create applications in minutes. |
1 versions
|
| flye | This module loads the PATH and other environment variables for flye version 2.9.5 |
4 versions
|
| fmt | fmt (formerly cppformat) is an open-source formatting library. It can be used as a safe alternative to printf or as a fast alternative to C++ IOStreams. |
7 versions
|
| focus | Focus is a package for High throughput processing of the image stacks recorded by electron microscopes. It acts as an interface between data collectuion and data processing for cryo-EM --focus launches the GUI --can also be run in command line mode |
2 versions
|
| foldseek | This package loads the environment for foldseek. |
1 versions
|
| fpm | fpm: Fortran Package Manager |
1 versions
|
| fpsync | This module provides the environment necessary to run fpsync, a data transfer tool that uses fpart and rsync to create parallel flows. To see options for use: fpsync -h |
1 versions
|
| frealign | This module sets the environment necessary to use frealing v9.11 |
1 versions
|
| frealix | This module sets the environment necessary to use frealix 1.1 |
1 versions
|
| freebayes | This module sets up the environment for the Cellbender package from the Broad Institute. To cite, please visit this page: https://github.com/broadinstitute/CellBender#citing-cellbender. |
4 versions
|
| freesurfer | This module loads the FreeSurfer path and environmental variables. If you also need Matlab (to run FS-FAST), also: cp $FREESURFER_HOME/startup.m ~/. module load matlab |
2 versions
|
| freetype | This module loads the PATH variable for FreeType (v. 2.5.5) |
1 versions
|
| freud | This module initializes the environment for Freud. Freud: Analysis software package for MD & MC simulation trajectories It has been installed with /usr/bin/python (2.7.5) |
1 versions
|
| fsl | FSL: Comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. |
3 versions
|
| funannotate | Container with Funannotate Run as "funannotate <arguments>" |
1 versions
|
| funtools | This module sets the environment for funtools, v 1.4.7: - Funtools is located in /uufs/chpc.utah.edu/sys/installdir/r8/funtools/1.4.7/bin and that directory is added to your PATH. |
1 versions
|
| galba | Container with GALBA Run as "galba.pl <arguments>" |
1 versions
|
| gamd-openmm | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
2 versions
|
| gamess | Sets the environmentable variables to run GAMESS using MPI Compiled with: intel and impi 2018.1.163 Support for NBO7 |
2 versions
|
| gamola2 | This module sets environment variables and loads required modules for the GAMOLA2 microbial genome annotation package. GAMOLA2 runs interactively as an X client, so make sure your ssh session provides X-windows forwarding (ie ssh -X login@hostname ...). GAMOLA2 should be run on a compute node via srun as it starts many compute- intensive programs. |
1 versions
|
| gams | This module sets the environment to run the GAMS software. This software requires a license file to load. You can load your license manually by using the command 'gamsgetkey' after loading the module. To check out a network license for a specified duration, use the -c or --checkout-duration option (with the duration defined in full hours) along with the -o or --output option (to specify the path for saving the license file). The generated license file will be valid for the designated period. Example: /path/to/GAMS/installation/directory/gamsgetkey xxyyzzxx-yyzz-xxyy-zzxx-yyzzxxyyzzxx -c 24 -o gamslice.txt |
1 versions
|
| gatk | This module provides the environment necessary to run java code GATK, verions 4.6. To run do 'gatk --help' to see options. requires jdk |
4 versions
|
| gaussian09 | This modulr provides the environment necessary for Gaussian09 |
2 versions
|
| gaussian16 | This module provides the environment necessary for Gaussian16 This SSE4 version is for the pre AVX nodes, and is the best version for the nodes on ember and lonepeak (outside of the onwer nodes on lonepeak) |
12 versions
|
| gautomatch | This module sets the environment necessary to use Gautomatch 0.56 To use: gautomatch |
1 versions
|
| gawk | (GNU) Awk is an interpreted programming language designed for text processing and typically used as a data extraction and reporting tool. It is a standard feature of most Unix-like operating systems. The GNU Awk manual can be found here: https://www.gnu.org/software/gawk/manual/gawk.html |
1 versions
|
| gcc | wxWidgets :: Cross-Platform GUI Library |
43 versions
|
| gcta | This package loads the environment to run gcta. To get syntaxon usage and options, enter 'gcta' at the command line . |
1 versions
|
| gctf | Module which sets the env. variables for the gctf package Look at contents of /uufs/chpc.utah.edu/sys/installdir/gctf/1.18_b2/bin for versions The Gctf_v1.18_b2_sm61_cu9.1 version is for use with GTX2080Ti, P40,or P100 gpus and the Gctf_v1.18_b2_sm70_cu9.1 version is for use with RTX2080Ti, V100, or TitanV gpus |
2 versions
|
| gdal | GDAL: Geospatial Data Abstraction Library. GDAL is a translator library for raster and vector geospatial data formats that is released under an MIT style Open Source License by the Open Source Geospatial Foundation. As a library, it presents a single raster abstract data model and single vector abstract data model to the calling application for all supported formats. It also comes with a variety of useful command line utilities for data translation and processing. |
12 versions
|
| gdc-client | This module loads the PATH and PYTHONPATH environment variables for gdc-client version 1.5.0. |
4 versions
|
| geant4 | Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science. |
8 versions
|
| gemma | GEMMA:Genome-wide Efficient Mixed Model Association (GEMMA) |
1 versions
|
| gempak | This module loads the GEMPAK 7.3.0 environment |
1 versions
|
| genai | Any help you want to display when running "module help module-name" |
2 versions
|
| geneious | Module which sets the PATH variable for Geneious. |
1 versions
|
| genomethreader | GenomeThreader is a gene structure prediction tool |
1 versions
|
| genometools | genometools is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. |
1 versions
|
| geomodelgrids | The GeoModelGrids project focuses on storing and querying georeferenced raster-based models with an emphasis on regional models. The models are composed of blocks, in which each block is a grid with a potentially different resolution that vary along the x, y, or z axis. EXECUTABLES: geomodelgrids_borehole geomodelgrids_info geomodelgrids_isosurface geomodelgrids_query geomodelgrids_queryelev DATA: stored in $GEOMODELDATA directory e.g.: geomodelgrids_info --all --models=$GEOMODELDATA/three-blocks-topo.h5 |
2 versions
|
| geotiff | This module loads: a. the PATH variable b. the MANPATH variable for geotiff (v.1.4.0) |
1 versions
|
| gffread | This package loads the environment to run gffread. |
1 versions
|
| gflags | The gflags package contains a C++ library that implements commandline flags processing. It includes built-in support for standard types such as string and the ability to define flags in the source file in which they are used. Online documentation available at: https://gflags.github.io/gflags/ |
1 versions
|
| gh | This module sets the PATH variable for GitHub CLI, the "gh" command. |
1 versions
|
| ghostscript | An interpreter for the PostScript language and for PDF. |
1 versions
|
| ginga | This module loads the PATH environment variable for ginga version 3.4.0. |
1 versions
|
| gisspa | GisSPA - GPU parallel for isSPA, pick particle with CC |
1 versions
|
| gistic2 | This module loads the PATH environment variable for GISTIC2 version 2.0.23. |
1 versions
|
| git | This module sets the PATH variable for Git (v. 2.23.0) |
2 versions
|
| git-crypt | This module sets the PATH variable for git-crypt (0.6.0) |
1 versions
|
| git-lfs | Git LFS is a system for managing and versioning large files in association with a Git repository. Instead of storing the large files within the Git repository as blobs, Git LFS stores special "pointer files" in the repository, while storing the actual file contents on a Git LFS server. |
2 versions
|
| glib | GLib provides the core application building blocks for libraries and applications written in C. The GLib package contains a low-level libraries useful for providing data structure handling for C, portability wrappers and interfaces for such runtime functionality as an event loop, threads, dynamic loading and an object system. |
2 versions
|
| glnexus | This module sets up GLnexus via a container. Based on DockerHub container quay.io/mlin/glnexus:v1.3.1 Run as "glnexus_cli" NOTE: This module does not work on the Lonepeak cluster, as it's CPUs are too old for it |
1 versions
|
| glog | C++ implementation of the Google logging module. |
2 versions
|
| gmap | This module sets up the environment for GMAP version 2019-09-12 |
1 versions
|
| gmp | GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers. |
3 versions
|
| gmsh | Gmsh is a free 3D finite element grid generator with a built-in CAD engine and post-processor. Its design goal is to provide a fast, light and user-friendly meshing tool with parametric input and advanced visualization capabilities. Gmsh is built around four modules: geometry, mesh, solver and post-processing. The specification of any input to these modules is done either interactively using the graphical user interface or in ASCII text files using Gmsh's own scripting language. |
2 versions
|
| gmt | GMT (Generic Mapping Tools) is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views. |
10 versions
|
| gmtsar | Loads the environment to use GMTSAR 5.6 a generic mapping tool; look in /uufs/chpc.utah.edu/sys/installdir/gmtsar/5.6/bin for tools. |
1 versions
|
| gnuplot | This module loads the gnuplot utility. To use, type "gnuplot". |
2 versions
|
| golang | This module loads the Go programming language module |
7 versions
|
| goldrush | This module loads the environment variables for goldrush version 1.1.0. |
2 versions
|
| google-cloud | This module defines path for Google Cloud SDK commands |
3 versions
|
| googletest | The google test module sets the following environmental variables: GTEST_DIR, GTEST_LIB, and GTEST_INC. It also modifies LD_LIBRARY_PATH |
3 versions
|
| gpt4all | This sets up GPT4All LLM workspace. Launch with the "chat" command. |
1 versions
|
| grace | This is the GRACE plotting program for X Windows. To start grace use "grace". GRACE requires the use of X11 forwarding; CHPC recommends using the FastX client for best performance. Please see https://www.chpc.utah.edu/documentation/software/fastx-x11.php for more information. |
1 versions
|
| grads | This module sets the variables for GrADS 2.2.2 |
3 versions
|
| grandslam | This module loads the environment to run GRAND-SLAM version 2.0.5. To use, there is program gedi, do gedi -h to see options |
1 versions
|
| graphicsmagick | Loads the environment to use graphicsmagick imaging processing tool version 1.4; to start use command gm, gm -help gives options. |
1 versions
|
| graphviz | This module sets the PATH variable for graphviz version 2.46.0. |
2 versions
|
| grass | GRASS GIS (Geographic Resources Analysis Support System), is a free and open source Geographic Information System (GIS) software suite used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization. |
6 versions
|
| grib | This loads the grib-api utilities. A list of command may be found here: https://software.ecmwf.int/wiki/display/GRIB/GRIB+tools |
1 versions
|
| gromacs | GROMACS is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers across the world. GROMACS is one of the fastest and most popular software packages available and can run on CPUs as well as GPUs. It is free, open source released under the GNU Lesser General Public License. Before the version 4.6, GROMACS was released under the GNU General Public License. |
70 versions
|
| grype | A vulnerability scanner for container images and filesystems |
1 versions
|
| gsl | The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite. |
7 versions
|
| guidance | This package loads the environment to run guidance version 2.02 which assignes confidence scores for alignments To see options do "perl $GUIDANCE_DIR/guidance.pl" |
1 versions
|
| guile | Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system. |
1 versions
|
| guppy | This module loads the PATH and other environment variables for guppy version 6.5.7 for GPU execution. |
8 versions
|
| gurobi | Gurobi is a mathematical Programming solver engine The following ENV. variables will be set when loading this module: GUROBI_HOME /uufs/chpc.utah.edu/sys/installdir/gurobi/9.0.3 In addition $GUROBI_HOME/bin will be added to $PATH $GUROBI_HOME/lib will be added to $LD_LIBRARY_PATH" |
2 versions
|
| gwasimulator | This module loads the PATH environment variable for GWAsimulator version 2.1. |
1 versions
|
| hadoop | This module loads the Hadoop enviornment (i.e. version 2.6.0) |
2 versions
|
| haplodmf | HaploDMF: viral haplotyps reconstruction from long reads via Deep Matrix Factorization |
1 versions
|
| haploview | This module provides the environment necessary to run java code haploview, version 4.2. requires jdk |
1 versions
|
| happy | This module sets up the environment to run the deeplearning environment version 2024.2.0. |
1 versions
|
| hashcat | This module sets the env. variables for hashcat hashcat --help A few examples can be found in: /uufs/chpc.utah.edu/sys/installdir/hashcat/3.5.0/share/doc/hashcat |
1 versions
|
| hdf-eos2 | HDF-EOS (Hierarchical Data Format - Earth Observing System) is a self- describing file format based upon HDF for standard data products that are derived from EOS missions. HDF-EOS2 is based upon HDF4. |
1 versions
|
| hdf4 | This module loads: a. the PATH variable b. the LD_LIBRARY variable for HDF4 (v.4.2.9) |
3 versions
|
| hdf5 | This module loads: a. the PATH variable b. the LD_LIBRARY variable for Parallel HDF5 (v.1.10.4) |
78 versions
|
| hdfview | This module sets the variables for HDFView 2.11 |
1 versions
|
| heasoft | This module sets up environment for HEASOFT versin 6.30.1. |
6 versions
|
| hichipper | This module sets up the environment to run hichipper version 0.7.7 . |
2 versions
|
| hicpro | This module sets up Hic-Pro container Based on Singularity recipe from https://github.com/nservant/HiC-Pro Run as "runbioBakery arguments". |
1 versions
|
| hipstr | HipSTR: Genotype and phase short tandem repeats using Illumina whole-genome sequencing data |
1 versions
|
| hisat | This package loads the environment to run hisat. To get syntaxon usage and options, enter 'hisat', 'hisat-build' or 'hisat-inspect' at the command line . |
1 versions
|
| hisat2 | This package loads the environment to run hisat2. To get syntax on usage and options, enter hisat2, hisat2-align-l, hisat2-align-s, hisat2-build, hisat2-build-l, hisat2-build-s, hisat2-inspect, hisat2-inspect-l, or hisat2-inspect-s at the command line. |
1 versions
|
| hmmer | HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). |
1 versions
|
| hmmer3 | This module sets the environment necessary to use hmmer, version 3.2.1 see contents of directory /uufs/chpc.utah.edu/sys/installdir/r8/hmmer/3.2.1 for different packages |
2 versions
|
| hoomd | HOOMD version 2.5.0, serial only, installed for compatibility with old projects. For new projects please use the latest HOOMD version. |
7 versions
|
| hoomd-blue | HOOMD-blue is a general-purpose particle simulation toolkit. It scales from a single CPU core to thousands of GPUs. You define particle initial conditions and interactions in a high-level python script. Then tell HOOMD-blue how you want to execute the job and it takes care of the rest. Python job scripts give you unlimited flexibility to create custom initialization routines, control simulation parameters, and perform in situ analysis. |
6 versions
|
| hpctoolkit | HPCToolkit is an integrated suite of tools for measurement and analysis of program performance on computers ranging from multicore desktop systems to the nation's largest supercomputers. By using statistical sampling of timers and hardware performance counters, HPCToolkit collects accurate measurements of a program's work, resource consumption, and inefficiency and attributes them to the full calling context in which they occur. |
3 versions
|
| hpl | HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark. |
14 versions
|
| hsi | This module sets the variables for HSI 4.0.1.3 |
1 versions
|
| htar | This module sets the variables for htar 4.0.1.3 |
1 versions
|
| htslib | C library for high-throughput sequencing data formats. |
4 versions
|
| hyphy | HyPhy: Hypothesis testing using Phylogenies |
6 versions
|
| hypre | Hypre is a library of high performance preconditioners that features parallel multigrid methods for both structured and unstructured grid problems. |
28 versions
|
| hysplit | This module sets up the environment for the HYSPLIT software package version 5.2.3. |
2 versions
|
| idba | IDBA is a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinfomatics |
1 versions
|
| idl | This module sets the variables for IDL 9.2 |
15 versions
|
| idr | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
1 versions
|
| idv | This module loads the PATH variable for IDV |
5 versions
|
| igv | This module loads the PATH environment variable for the Integrated Genome Viewer (IGV) version 2.8.2. To run IGV execute the command "igv.sh". |
1 versions
|
| ihrsr | This module loads the PATH for IHRSR++ version 1.5. This software also uses spiderweb version 21.02. |
1 versions
|
| ilastik | This module loads the PATH environment variable for ilastik-1.4.0.post1-gpu-Linux. run_ilastik.sh --help run_ilastik.sh # start GUI |
1 versions
|
| imagej | ImageJ Java-based image processing program Executable Name: ImageJ |
1 versions
|
| imagemagick | ImageMagick is a software suite to create, edit, compose, or convert bitmap images. |
2 versions
|
| imod | This module sets the environment for IMOD |
4 versions
|
| impi | Sets up the environment for IMPI, Intel's version if the MPI libraries. Part of the intel cluster studio. |
6 versions
|
| indelminer | This module loads the PATH environment variable for indelminer version 0.2. |
1 versions
|
| infernal | This module provides the environment necessary to run infernal (INFERence of RNA ALignment) version 1.1.1. |
1 versions
|
| inparanoid | This module sets the environment necessary to use inparanoid |
1 versions
|
| inrich | This module sets the environment necessary to use inrich version 1.1 Usage: inrich -a "associated_interval_file" -t "target_gene_set_file" -m "reference_SNP_file" -g "reference_gene_file" Note there are other optional inputs; see http://atgu.mgh.harvard.edu/inrich/resources/InRich.Cmd.Manual.pdf for details |
1 versions
|
| inspector | This module sets the variables for Intel Inspector |
1 versions
|
| instantclient | Oracle Instant Client v. 18.5.0.0.0 contains the following modules: a. basic b. sqlplus c. tools d. sdk e. jdbc f. odbc |
1 versions
|
| intel | This module loads the Intel compiler path and environmental variables |
11 versions
|
| intel-mkl | Intel Math Kernel Library. |
18 versions
|
| intel-mpi | Intel MPI |
22 versions
|
| intel-oneapi-advisor | Intel Advisor is a design and analysis tool for developing performant code. The tool supports C, C++, Fortran, SYCL, OpenMP, OpenCL code, and Python. It helps with the following: Performant CPU Code: Design your application for efficient threading, vectorization, and memory use. Efficient GPU Offload: Identify parts of the code that can be profitably offloaded. Optimize the code for compute and memory. LICENSE INFORMATION: By downloading and using this software, you agree to the terms and conditions of the software license agreements at https://intel.ly/393CijO. |
2 versions
|
| intel-oneapi-compilers | Intel OneAPI compilers Provides Classic and Beta compilers for: Fortran, C, C++ |
7 versions
|
| intel-oneapi-inspector | Intel Inspector is a dynamic memory and threading error debugger for C, C++, and Fortran applications that run on Windows and Linux operating systems. Save money: locate the root cause of memory, threading, and persistence errors before you release. Save time: simplify the diagnosis of difficult errors by breaking into the debugger just before the error occurs. Save effort: use your normal debug or production build to catch and debug errors. Check all code, including third-party libraries with unavailable sources. LICENSE INFORMATION: By downloading and using this software, you agree to the terms and conditions of the software license agreements at https://intel.ly/393CijO. |
1 versions
|
| intel-oneapi-itac | The Intel Trace Analyzer and Collector profiles and analyzes MPI applications to help focus your optimization efforts. Find temporal dependencies and bottlenecks in your code. Check the correctness of your application. Locate potential programming errors, buffer overlaps, and deadlocks. Visualize and understand parallel application behavior. Evaluate profiling statistics and load balancing. Analyze performance of subroutines or code blocks. Learn about communication patterns, parameters, and performance data. Identify communication hot spots. Decrease time to solution and increase application efficiency. LICENSE INFORMATION: By downloading and using this software, you agree to the terms and conditions of the software license agreements at https://intel.ly/393CijO. |
1 versions
|
| intel-oneapi-mkl | Intel oneAPI MKL. |
43 versions
|
| intel-oneapi-mpi | Intel oneAPI MPI. |
32 versions
|
| intel-oneapi-tbb | Intel oneAPI Threading Building Blocks (oneTBB) is a flexible performance library that simplifies the work of adding parallelism to complex applications across accelerated architectures, even if you are not a threading expert. LICENSE INFORMATION: By downloading and using this software, you agree to the terms and conditions of the software license agreements at https://intel.ly/393CijO. |
8 versions
|
| intel-oneapi-vtune | Intel VTune Profiler is a profiler to optimize application performance, system performance, and system configuration for HPC, cloud, IoT, media, storage, and more. CPU, GPU, and FPGA: Tune the entire application's performance--not just the accelerated portion. Multilingual: Profile SYCL, C, C++, C#, Fortran, OpenCL code, Python, Google Go programming language, Java, .NET, Assembly, or any combination of languages. System or Application: Get coarse-grained system data for an extended period or detailed results mapped to source code. Power: Optimize performance while avoiding power and thermal-related throttling. LICENSE INFORMATION: By downloading and using this software, you agree to the terms and conditions of the software license agreements at https://intel.ly/393CijO. |
1 versions
|
| intelpy | Intel Python 3.6.3 To check the installed packages: pip list --format=columns |
2 versions
|
| interconnect | This module sets the environment necessary to run lumerical interconnect To start interface, fdtd-solutions |
1 versions
|
| interproscan | This module sets the variables for InterProScan. Run as interproscan.sh |
2 versions
|
| ioapi | Models-3/EDSS Input/Output Applications Programming Interface. |
6 versions
|
| ipp | This module loads the Intel Integrated Performance Primitives |
1 versions
|
| ippcp | This module loads the Intel Integrated Performance Primitives Cryptography |
1 versions
|
| iqtree | This module sets the PATH variable for IQ-TREE2 |
3 versions
|
| irazu | To start Irazu run "irazu_user_interface" |
1 versions
|
| isce | This module sets up the environment for the ISCE software package version 2.4. |
3 versions
|
| isonet |
2 versions
|
|
| isoseq | This module loads the PATH and PYTHONPATH environment variables for isoseq version 4.0.0. |
1 versions
|
| itac | This module sets the variables for Intel Trace Analyzer and Collector |
3 versions
|
| itasca | Any help you want to display when running "module help module-name" |
3 versions
|
| jags | JAGS - Just Another Gibbs Sampler To check pkg-config, use e.g.: pkg-config jags --help pkg-config jags --libs |
1 versions
|
| jalview | This module provides the environment necessary to run java code JalView 2.9.0b2. To run: Jalview |
1 versions
|
| jdk | This module loads the env. variables for JAVA (v. 1.8.0_xxx) shipped with Rocky 8 For help on keyword \in {java, javac, jar, jdb, javadoc, appletviewer, javapackager, jinfo, ...} man $keyword |
3 versions
|
| jellyfish | Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. Run it with the command "jellyfish". More information is available here: http://www.genome.umd.edu/jellyfish.html |
4 versions
|
| juicer | This module sets up the environment for juicer version 1.5.6. To run the code see this page at the NIH: https://hpc.nih.gov/apps/juicer.html or on GitHub: https://github.com/aidenlab/juicer/wiki |
1 versions
|
| julia | Julia - 1.2.0 Using MKL (Intel 18.1.163) |
10 versions
|
| juno | Module to set the Environmental Variables for Juno 0.20.1 |
1 versions
|
| k8 | k8: JavaScript runtime built on top of Google's v8 JavaScript engine EXECUTABLE: k8 |
1 versions
|
| kallisto | This package loads the environment to run kallisto. To get syntaxon usage and options, enter 'kallisto' at the command line . |
2 versions
|
| kim-api | OpenKIM is an online framework for making molecular simulations reliable, reproducible, and portable. Computer implementations of inter- atomic models are archived in OpenKIM, verified for coding integrity, and tested by computing their predictions for a variety of material properties. Models conforming to the KIM application programming interface (API) work seamlessly with major simulation codes that have adopted the KIM API standard. This package provides the kim-api library and supporting utilities. It also provides a small set of example models. To obtain all models archived at https://openkim.org that are compatible with the kim-api package, install and activate the openkim- models package too. |
6 versions
|
| king | This module sets the path for the 2.3.2 KING (Kinship-based INference for Gwas) installation |
2 versions
|
| kraken2 | This module sets the environment for kraken2 version 2.1.6. |
3 versions
|
| kronatools | Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files. The executables are to be found in: /uufs/chpc.utah.edu/sys/installdir/r8/kronatools/2.8.1/bin The taxonomy is stored in: /uufs/chpc.utah.edu/sys/installdir/r8/kronatools/2.8.1/taxonomy |
1 versions
|
| ksnp4 | run: kSNP4 -h |
1 versions
|
| labgym | Start LabGym with GUI: LabGym |
1 versions
|
| lammps | LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. This package uses patch releases, not stable release. See https://github.com/spack/spack/pull/5342 for a detailed discussion. |
51 versions
|
| lastz | This module sets up the PATH variable for LASTZ package |
1 versions
|
| launcher | This module initializes the environment variables for launcher version 3.1.1. https://github.com/TACC/launcher Launcher is a utility for performing simple, data parallel, high throughput computing (HTC) workflows on clusters, massively parallel processor (MPP) systems, workgroups of computers, and personal machines. |
1 versions
|
| ldhat | This module sets the environment for ldhat version 2.2a: - The software is located in /uufs/chpc.utah.edu/sys/installdir/ldhat/2.2a, and that directory is added to your PATH. - That directory name is also stored in the environment variable LDHAT. - The precomputed tables have been download and are located in $LDHAT/lk_files . |
1 versions
|
| lftp | LFTP is a sophisticated file transfer program supporting a number of network protocols (ftp, http, sftp, fish, torrent). |
1 versions
|
| libarchive | libarchive -- development library for archiving tools. |
1 versions
|
| libbeagle | Beagle performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection. |
1 versions
|
| libedit | An autotools compatible port of the NetBSD editline library |
1 versions
|
| libint | Libint is a high-performance library for computing Gaussian integrals in quantum mechanics. |
1 versions
|
| libjpeg | libjpeg is a widely used free library with functions for handling the JPEG image data format. It implements a JPEG codec (encoding and decoding) alongside various utilities for handling JPEG data. |
1 versions
|
| libpng | libpng is the official PNG reference library. |
1 versions
|
| libtheora | Theora Video Compression. |
2 versions
|
| libtool | libtool -- library building part of autotools. |
29 versions
|
| libuv | Multi-platform library with a focus on asynchronous IO |
1 versions
|
| libvips | libvips is a demand-driven, horizontally threaded image processing library. Compared to similar libraries, libvips runs quickly and uses little memory. |
1 versions
|
| libxml2 | libxm2 - 2.9.9 to parse XML documents |
3 versions
|
| libxsmm | Library targeting Intel Architecture for specialized dense and sparse matrix operations, and deep learning primitives. |
1 versions
|
| liggghts | Discrete element method particle simulation. |
2 versions
|
| likwid | This module loads environment for Likwid. Do not use shared partitions to run jobs with likwid. |
2 versions
|
| lipidens | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
1 versions
|
| llvm | The LLVM Project is a collection of modular and reusable compiler and toolchain technologies. Despite its name, LLVM has little to do with traditional virtual machines, though it does provide helpful libraries that can be used to build them. The name "LLVM" itself is not an acronym; it is the full name of the project. |
11 versions
|
| log4cplus | log4cplus is a simple to use C++ logging API providing thread-safe, flexible, and arbitrarily granular control over log management and configuration. |
1 versions
|
| longranger | Long Ranger is a package from 10X Genomics for SNP, indel, and structural variant calling in WGS and targeted genome sequence data. |
1 versions
|
| lsdyna | This module sets the environment to run the version of LS-DYNA version 10.1.0; to run use command lsdyna. |
34 versions
|
| lumerical | This module sets the environment necessary to run Lumerical suite of programs version 2020a To start interface, fdtd-solutions, mode-solutions,... |
7 versions
|
| lumerical-device | This module sets the environment necessary to run Lumerical DEVICE version 7.3.1854 To start interface, run "device" |
1 versions
|
| lumerical-mode | This module sets the environment necessary to run Lumerical MODE Solutions To start interface, run "device" |
1 versions
|
| lymph | This module sets the PATH variable for Lymph (WITH GPU support). Works ONLY in BASH. To START: source activate fsm_tftpidx To TEST: python3 >>> import tensorflow as tf >>> tf.__version__ >>> tf.test.is_gpu_available() To STOP: source deactivate |
1 versions
|
| lz4 | This module loads the PATH variable for lz4 (r127) |
1 versions
|
| macau | This module loads the PATH environment variable for macau version 1.40. |
1 versions
|
| macs | This module loads the PATH and PYTHONPATH environment variables for MACS version 2.2.7.1 |
3 versions
|
| maestro | This module sets the environment necessary to use Schrodinger maestro interface (free academic version). To start use $SCHRODINGER/maestro OR on a frisco5/6 or another node with graphics capabilities use vglrun $SCHRODINGER/maesto |
1 versions
|
| maffilter | This module sets the PATH variable for maffilter (v.1.3.1) |
1 versions
|
| mafft | This module loads the PATH environment variable for mafft version 7.407. |
2 versions
|
| maftools | MafTools (Multiple ALignment Format Tools |
1 versions
|
| magic | This module loads the R and python modules, and sets the PYTHONPATH environment variables for Rmagic version 1.4.0. |
1 versions
|
| magma | MAGMA: Matrix Algebra for GPU and Multicore Architectures This modules sets the following environmental variables: MAGMA_DIR /uufs/chpc.utah.edu/sys/installdir/magma/2.3.0-i18.1-cuda9.1 MAGMA_INCDIR /uufs/chpc.utah.edu/sys/installdir/magma/2.3.0-i18.1-cuda9.1/include MAGMA_LIBDIR /uufs/chpc.utah.edu/sys/installdir/magma/2.3.0-i18.1-cuda9.1/lib Please read the README.txt: /uufs/chpc.utah.edu/sys/installdir/magma/2.3.0-i18.1-cuda9.1/README.txt The CFLAGS & LDFLAGS are to be found in README.txt as well in /uufs/chpc.utah.edu/sys/installdir/magma/2.3.0-i18.1-cuda9.1/lib/pkgconfig/magma.pc |
1 versions
|
| maker | This module sets the environment to run maker version 3.01.04. |
2 versions
|
| malamute | run: malamute-opt --help |
2 versions
|
| manta | manta: Structural variant and indel caller for mapped sequencing data |
1 versions
|
| marvin | This load the Marvin Suite of tools, by ChemAxon. Marvin has three primary tools, MarvinSketch, MarvinSpace, and MarvinView, as well as StructureChecker. All of them require access via X11. CHPC recommends the use of the FastX client; more information can be found here: https://www.chpc.utah.edu/documentation/software/fastx-x11.php The Marvin Suite has tools that require a license, which is freely available to academic users. Please see the following page for more information on acquiring a license: https://www.chpc.utah.edu/documentation/software/marvinsketch.php |
1 versions
|
| masurca | MaSuRCA is whole genome assembly software package |
1 versions
|
| mathematica | This module loads the Mathematica v. 14.2.1 environment Revision History: https://www.wolfram.com/mathematica/quick-revision-history.html See also: https://writings.stephenwolfram.com/2025/01/launching-version-14-2-of-wolfram-language-mathematica-big-data-meets-computation-ai/ |
12 versions
|
| matlab | This module sets the variables for Matlab R2023b |
22 versions
|
| maven | This module loads the Maven path and environmental variables (v. 3.3.3) |
1 versions
|
| maxquant | MaxQuant To invoke: CMD LINE: mono $MAXQUANT/bin/MaxQuantCmd.exe --help GUI : mono $MAXQUANT/bin/MaxQuantGui.exe |
1 versions
|
| medaka | medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. For more information see https://github.com/nanoporetech/medaka |
4 versions
|
| medea | This package loads the MedeA molecular simulation toolkit. To start the program, use 'MedeA' at the command line. |
2 versions
|
| mega2 | Module which sets the PATH variable for mega2. |
2 versions
|
| megadetector | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
1 versions
|
| megalodon | This module loads the PATH and PYTHONPATH environment variables for megalodon version 2.3.3. |
1 versions
|
| membrainseg | This module sets up the miniforge3 environment for the MemBrain-Seg package. |
1 versions
|
| meme | The MEME Suite Motif-based sequence analysis tools |
5 versions
|
| mercurial | Mercurial is a free, distributed source control management tool. The binary is named 'hg' hg --help |
1 versions
|
| merlin | This module sets the environment necessary to use merlin version 1.1.2 |
1 versions
|
| mesa | Modules for Experiments in Stellar Astrophysics (MESA) (1D Stellar Evolution Code) Note: The variable OMP_NUM_THREADS can be overwritten on the cmd line / in a SLURM script. |
3 versions
|
| mesasdk | This module loads the mesa-sdk environmental (including the gcc compilers and auxiliary libraries) |
2 versions
|
| meshroom | This package loads the Meshroom 3D reconstruction software. To start the program, in the command line, run 'vglrun -c proxy Meshroom'. Note that this only works on interactive nodes with OpenGL GPUs. |
1 versions
|
| meson | Meson Build System - (built with python 3.6.3) Executable: meson |
12 versions
|
| metahipmer | Run as "mhm2.py [arguments]". This Python wrapper script will pick up SLURM job parameters. |
1 versions
|
| metamap | This module provides the environment necessary to run metamap, 2020v1 version |
2 versions
|
| metamaplite | This module provides the environment necessary to run metamaplite, version 3.6.2rc8 |
1 versions
|
| metaminimac2 | MetaMinimac2 is an efficient tool to combine genotype data imputed against multiple reference panels. |
1 versions
|
| metaphlan | This module sets up MetaPhlAn container. Based on biocontainers container docker://quay.io/biocontainers/metaphlan:4.1.1--pyhdfd78af_0 Run as "metaphlan arguments". Shell to the container is available as "startmetaphlan" |
2 versions
|
| metawrap | MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis metawrap --help --show-config |
2 versions
|
| metis | METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. |
3 versions
|
| mgltools | This module loads the env to run MGLTools, version 1.5.7 |
1 versions
|
| microbecensus | This module sets up the environment for the microbecensus anaconda environment version 1.1.1. |
1 versions
|
| miniconda3 | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
7 versions
|
| miniforge3 | Base Miniforge3 for user python environments Create new environment: mamba create -n myenv -c conda-forge Activate environment: conda activate myenv List available environments: mamba env list For more information see: |
2 versions
|
| minimap2 | This module sets up the environment necessary to use minimap2 version 2.24. |
2 versions
|
| minionqc | Module which sets the PATH variable for minionqc. |
1 versions
|
| mira | This module sets the environment necessary to use mira version v5rc2. |
1 versions
|
| miranda | This package loads the environment to run miRanda version 3.3a. To get syntaxon usage and options, enter 'miranda' at the command line. |
1 versions
|
| mirdeep-star | This module provides the environment necessary to run miRDeep*, version 37. |
1 versions
|
| mirdeep2 | This module sets the environment necessary to use miRDeep2, version 2.0.0.8 To run after loading module do "mirdeep2.pl" |
1 versions
|
| mirge | This module sets up the environment for the miRge software package version 2.0. |
1 versions
|
| miriad | This module loads evironment for Miriad |
1 versions
|
| mixcr | MiXCR is a universal software for fast and accurate analysis of raw T- or B- cell receptor repertoire sequencing data. |
1 versions
|
| mixmhcpred | MixMHCpred3.0 is a pan-Allele predictor designed for predicting peptide bindings to MHC alleles and can also perform sequence alignment and binding motif plotting. This module is based on the latest version of the master Git branch. |
1 versions
|
| mixtcrpred | MixTCRpred accurately predicts T-cell receptors (TCRs) recognizing several viral and cancer epitopes (peptides displayed on MHC molecules or pMHCs) This module was made with the latest version of the software on the main GitHub branch. |
1 versions
|
| mkl | This module loads the Intel Math Kernel Library environmental variables For linking instructions see https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor or run mkl_link_tool |
3 versions
|
| mmseqs2 |
1 versions
|
|
| mmv | Move/Copy/Append/Link multiple files mmv is a program to move/copy/append/link multiple files according to a set of wildcard patterns. This multiple action is performed safely, i.e. without any unexpected deletion of files due to collisions of target names with existing filenames or with other target names. |
1 versions
|
| model-angelo | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
2 versions
|
| modeller | This module provides the environment necessary for Modeller 9.9 |
2 versions
|
| molden | A package for displaying Molecular Density from various Ab Initio packages |
1 versions
|
| mono | This module loads the Mono compiler path and environmental variables (v. 6.8.0) on Centos7 |
2 versions
|
| moose | Module which sets the PATH variable for MOOSE (conda env) To check help page: moose --help |
2 versions
|
| mopac | This modulr provides the environment necessary for MOPAC2012 |
1 versions
|
| mosdepth | Mosdepth is a fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing |
1 versions
|
| mosek | Mosek v. 8.0.0.60 |
1 versions
|
| mothur | This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. |
3 versions
|
| motioncor2 | Module which sets the env. variables for the motioncr2 package NOTE - there are 10 different executables, built with diffferent CUDA version: MotionCor2_1.6.3_Cuda101_Feb18_2023 MotionCor2_1.6.3_Cuda102_Feb18_2023 MotionCor2_1.6.3_Cuda111_Feb18_2023 MotionCor2_1.6.3_Cuda112_Feb18_2023 MotionCor2_1.6.3_Cuda113_Feb18_2023 MotionCor2_1.6.3_Cuda114_Feb18_2023 MotionCor2_1.6.3_Cuda115_Feb18_2023 MotionCor2_1.6.3_Cuda116_Feb18_2023 MotionCor2_1.6.3_Cuda117_Feb18_2023 MotionCor2_1.6.3_Cuda118_Feb18_2023 |
4 versions
|
| motioncor3 | Run as MotionCor3 |
1 versions
|
| mpfr | The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. |
1 versions
|
| mpich | This module loads the env. variables for the MPICH2 library (v.3.3) |
24 versions
|
| mpich2 |
1 versions
|
|
| mplus | This module sets the environment necessary to run mplus 8.3 |
1 versions
|
| mrbayes | MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters. |
2 versions
|
| mropen | This module sets a few ENVIRONMENTAL variables for R 3.5.1 i.e. "Feather Spray" (Revolution Analytics) To modify #threads (default multithreaded), you need to set the OMP_NUM_THREADS env. variable according to the #cores on the compute node, e.g.: export OMP_NUM_THREADS=12 (Bash) setenv OMP_NUM_THREADS 12 (Tcsh) |
1 versions
|
| mrsfast | Module which sets the PATH variable for MOOSE (conda env) To check help page: moose --help |
1 versions
|
| mrtrix3 | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
1 versions
|
| multiqc | Sets up the environment for the MultiQC command. MultiQC is documented here: http://multiqc.info/ |
3 versions
|
| mummer4 | MUMmer is a versatil alignment tool for DNA and protein sequences. |
1 versions
|
| mumps | MUMPS: a MUltifrontal Massively Parallel sparse direct Solver |
8 versions
|
| muscle | To check help page: muscle --help |
1 versions
|
| mvapich | Mvapich is a High-Performance MPI Library for clusters with diverse networks (InfiniBand, Omni-Path, Ethernet/iWARP, and RoCE) and computing platforms (x86 (Intel and AMD), ARM and OpenPOWER) |
1 versions
|
| mvapich2 | This module loads the env. variables for the MVAPICH2 library (v.2.2) compiled with intel/2018.2.187 |
19 versions
|
| mysql | MySQL is an open source relational database management system. |
1 versions
|
| namd | This module sets the variables for NAMD NOTE: Still have to specify the full path to the namd2 executable |
12 versions
|
| nanopolish | Software package for signal-level analysis of Oxford Nanopore sequencing data. |
1 versions
|
| nanopore | This module sets up the environment for the nanopore collection of software version 1.0. |
1 versions
|
| napari-boxmanager | napari-boxmanager: Particle selection tool for cryo-em EXECUTABLE: napari_boxmanager |
1 versions
|
| nbodykit | This modules sets up the PATH and PYTHONPATH environment variables for the nbodykit package version 0.3-dev. |
1 versions
|
| ncarg | This module loads the NCARG 6.2.1 environment |
1 versions
|
| ncbi-rmblastn | RMBlast search engine for NCBI |
1 versions
|
| ncbrowse | This module sets the variables for RncNCBrowse |
1 versions
|
| nccl | NCCL: NVIDIA Collective Communication Library NCCL provides routines such as all-gather, all-reduce, broadcast, reduce, reduce-scatter as well as point-to-point send and receive that are optimized to achieve high bandwidth and low latency over PCIe and NVLink high-speed interconnects within a node and over NVIDIA Mellanox Network across nodes. |
8 versions
|
| nccmp | Compare NetCDF Files |
2 versions
|
| ncdu | ncdu :: disk usage analyzer with a text-mode user interface. |
1 versions
|
| ncftp | This module sets the variables for ncftp 3.2.5 |
1 versions
|
| ncl | This module loads the NCL-NCARG 6.6.2 environment |
1 versions
|
| nco | The NCO toolkit manipulates and analyzes data stored in netCDF- accessible formats |
1 versions
|
| ncview | This module sets the variables for NCView |
1 versions
|
| netcdf | This module sets up environment of combined NetCDF-C, NetCDF-Fortran and HDF5 |
4 versions
|
| 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. This is the C distribution. |
81 versions
|
| netcdf-cxx | This module loads: a. the PATH variable b. the LD_LIBRARY variable for the netCDF-cxx package (v.4.3.0) |
18 versions
|
| netcdf-f | This module loads: a. the PATH variable b. the LD_LIBRARY variable c. sets the following Environmental Variables NETCDF_INCFDIR (Header Files Fortran Library) NETCDF_LIBFDIR (Fortran Library) for the NetCDF-f package (v.4.4.4) |
4 versions
|
| netcdf-fortran | 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. This is the Fortran distribution. |
43 versions
|
| netlib-scalapack | ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines |
24 versions
|
| netpbm | This module sets environment for netpbm library and packages |
1 versions
|
| nextflow | This module loads the PATH environment variable and sets up the java environment for nextflow (23.10.0.5889) |
7 versions
|
| ngc | Nvidia GPU Cloud Command Line Interface (NGC CLI) |
1 versions
|
| ngen | This module provides the environment necessary to run NOAA's ngen - Next Generation Water Modeling Engine and Framework Prototype, verions 0.3.0. To run, use the command 'ngen --help' to see options. |
1 versions
|
| ngsep | This module sets up the environment for NGSEP, a Java program for analysis of next generation DNA sequencing data. This module defines the NGSEPDIR environment variable, which is the location of the NGSEPcore_4.0.0.jar file, and sets the alias "ngsep" to the command "java -jar $NGSEPDIR/NGSEPcore_4.0.0.jar". For more information see https://sourceforge.net/projects/ngsep . |
1 versions
|
| ngspeciesid | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
1 versions
|
| ngstools | This module provides the environment necessary to run ngsTools, a set of program to analyze NGS data for population genetics purposes. See https://github.com/mfumagalli/ngsTools/blob/master/TUTORIAL.md to get started |
1 versions
|
| ngsutils | run: ngsutils help CMD |
1 versions
|
| ninja | Ninja is a small build system with a focus on speed. It differs from other build systems in two major respects: it is designed to have its input files generated by a higher-level build system, and it is designed to run builds as fast as possible. |
7 versions
|
| nlloc | This is the module to set the environment to run NonLinLoc, a package for Probabilistic, Non-Linear, Global-Search Earthquake Location in 3D Media See http://alomax.free.fr/nlloc/soft7.00/index.html for information Run using any of the binary names found in /uufs/chpc.utah.edu/sys/installdir/nlloc/7.00/bin |
1 versions
|
| nlopt | NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. |
1 versions
|
| nmrfam-sparky | This module loads the PATH and PYTHONPATH environment variables for nmrfam-sparky package version 1.2. |
1 versions
|
| node-js | Node.js is an open-source, cross-platform JavaScript runtime environment. |
2 versions
|
| nodejs | Node.js is an open-source, cross-platform JavaScript runtime environment commonly used for server-side programming and building backend services |
2 versions
|
| npm | npm: A package manager for javascript. |
3 versions
|
| ntcard | This package loads the environment to run ntCard, version 1.2.2. |
1 versions
|
| nvhpc | The NVIDIA HPC SDK is a comprehensive suite of compilers, libraries and tools essential to maximizing developer productivity and the performance and portability of HPC applications. The NVIDIA HPC SDK C, C++, and Fortran compilers support GPU acceleration of HPC modeling and simulation applications with standard C++ and Fortran, OpenACC directives, and CUDA. GPU-accelerated math libraries maximize performance on common HPC algorithms, and optimized communications libraries enable standards-based multi-GPU and scalable systems programming. Performance profiling and debugging tools simplify porting and optimization of HPC applications. |
15 versions
|
| nvim | NeoVim :: hyperextensible Vim-based text editor executable :: nvim |
2 versions
|
| nvtop | This module provides the environment necessary to run nvtop. To see options for use: 'man nvtop' |
1 versions
|
| nwchem | Module file for nwchem 6.3 ash mvapich2/intel installation; AMO |
15 versions
|
| octave | GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. It may also be used as a batch-oriented language. |
8 versions
|
| oic | Oracle Client Shared Library 64-bit |
1 versions
|
| old | LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. This package uses patch releases, not stable release. See https://github.com/spack/spack/pull/5342 for a detailed discussion. |
2 versions
|
| olex | Module which sets the env. variables for olex The main executable: start |
1 versions
|
| ollama | Ollama :: Tool to run large language models (LLMs) directly on a local machine EXE : ollama HELP: ollama --help FAQ : https://github.com/ollama/ollama/blob/main/docs/faq.md |
6 versions
|
| omega-h | Omega_h is a C++11 library providing data structures and algorithms for adaptive discretizations. Its specialty is anisotropic triangle and tetrahedral mesh adaptation. It runs efficiently on most modern HPC hardware including GPUs. |
4 versions
|
| oncotator | Oncotator tool for annotating human genomic point mutations and indels with data relevant to cancer researchers. The Data Source is stored in DATA_DIR (env. variable) DATA_DIR := /uufs/chpc.utah.edu/sys/installdir/oncotator/2.7.11-c7/1.9.3.0/oncotator_v1_ds_April052016 Binaries: ======== oncotator -h initializeDatasource |
1 versions
|
| openbabel | Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. |
3 versions
|
| openblas | OpenBLAS: An optimized BLAS library |
11 versions
|
| opencoarrays | OpenCoarrays is an open-source software project that produces an application binary interface (ABI) supporting coarray Fortran (CAF) compilers, an application programming interface (API) that supports users of non-CAF compilers, and an associated compiler wrapper and program launcher. |
1 versions
|
| opencv | OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. |
2 versions
|
| openfoam | OpenFOAM is a GPL-opensource C++ CFD-toolbox. This offering is supported by OpenCFD Ltd, producer and distributor of the OpenFOAM software via www.openfoam.com, and owner of the OPENFOAM trademark. OpenCFD Ltd has been developing and releasing OpenFOAM since its debut in 2004. |
12 versions
|
| openfoam-org | OpenFOAM is a GPL-opensource C++ CFD-toolbox. The openfoam.org release is managed by the OpenFOAM Foundation Ltd as a licensee of the OPENFOAM trademark. This offering is not approved or endorsed by OpenCFD Ltd, producer and distributor of the OpenFOAM software via www.openfoam.com, and owner of the OPENFOAM trademark. |
2 versions
|
| openjdk | The free and opensource java implementation |
5 versions
|
| openkim-models | OpenKIM is an online framework for making molecular simulations reliable, reproducible, and portable. Computer implementations of inter- atomic models are archived in OpenKIM, verified for coding integrity, and tested by computing their predictions for a variety of material properties. Models conforming to the KIM application programming interface (API) work seamlessly with major simulation codes that have adopted the KIM API standard. This package provides all models archived at openkim.org that are compatible with the kim-api package. |
3 versions
|
| openmkm | This module loads the various modules and sets environment variables for OpenMKM version 0.3. Once the module has loaded, the OpenMKM "omkm" program will be on your path. Examples are located in: /uufs/chpc.utah.edu/sys/installdir/openmkm/0.3/openmkm-0.3/Data/examples |
1 versions
|
| openmm | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
1 versions
|
| openmolcas | OpenMolcas is a quantum chemistry software package. The key feature of OpenMolcas is the multiconfigurational approach to the electronic structure. |
2 versions
|
| openmpi | An open source Message Passing Interface implementation. The Open MPI Project is an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available. Open MPI offers advantages for system and software vendors, application developers and computer science researchers. |
105 versions
|
| opensees | Module which loads the environment for OpenSEES |
6 versions
|
| openssh-hpn | This module provides the environment necessary to run openssh (with HPN patch set), see ssh --help for more info. |
1 versions
|
| openvino | This module loads the OpenVINO 2023.1 environment |
1 versions
|
| oradecompression | DRAGEN ORA Decompression Software decompresses fastq.ora files into fastq.gz files. Fastq.ora files are generated using lossless compression technology as part of DRAGEN. Orad is the executable file that runs the DRAGEN ORA Decompression Software, which is a standalone piece of software. |
1 versions
|
| orca | ORCA - Quantum Chemistry Suite Tutorials: https://www.faccts.de/docs/orca/6.0/tutorials/ Manual: /uufs/chpc.utah.edu/sys/installdir/r8/orca/6.0.1/doc/manual.pdf |
10 versions
|
| orthofinder | This module sets up the environment to run orthofinder version 2.5.4 from https://hub.docker.com/r/davidemms/orthofinder by aliasing the container call to the orthofinder executable. |
1 versions
|
| ovito | This module sets up the environment to run ovito. The program must be run on a node with a graphic card (most general ints, frisco nodes). To run: ml ovito vglrun -c proxy ovito |
3 versions
|
| p4vasp | This module runs p4vasp via a Singularity container Run as "p4v" |
1 versions
|
| p7zip | A Unix port of the 7z file archiver |
1 versions
|
| packmol | This module provides the environment necessary for packmol 14.255 |
1 versions
|
| paml | Module which sets the PATH variable for paml package. |
2 versions
|
| pandas | This module loads the anaconda environment for pandas version 1.3.1 |
1 versions
|
| pandaseq | PANDAseq assembles Illumina Solexa overlapping pair-end reads. More informaiton can be obtained at https://github.com/neufeld/pandaseq/wiki/PANDAseq-Assembler |
1 versions
|
| pandoc | This module sets the PATH variable for Pandoc 2.19.2 Executables: pandoc |
2 versions
|
| pannzer | This module loads the PATH environment variable and loads other modules for pannzer version 3.0. |
1 versions
|
| papi | This module sets the following env. variables: a. PATH b. LD_LIBRARY_PATH c. the MANPATH variable You can invoke the man page as follows: man 3 netcdf d. The following env. variables: PAPI_DIR :: root directory of PAPI installation PAPI_INCDIR :: directory with header files PAPI_LIBDIR :: directory with libraries for the PAPI (v.5.6.0) for Centos7 |
1 versions
|
| parallel | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input. |
3 versions
|
| parallel-netcdf | PnetCDF (Parallel netCDF) is a high-performance parallel I/O library for accessing files in format compatibility with Unidata's NetCDF, specifically the formats of CDF-1, 2, and 5. |
26 versions
|
| paraview | Module which sets the PATH variable for paraview. Run either with OpenGL via "vglrun -c proxy paraview", or as "paraview --mesa" to use Mesa based CPU rendering. |
4 versions
|
| 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. |
2 versions
|
| pasa | This module creates shell functions or aliases for a long list of commands that are part of the PASA pipeline including the Launch_PASA_pipeline.pl script, all of which can be called from the shell, and all of which are found in the Apptainer container /uufs/chpc.utah.edu/sys/installdir/r8/pasa/2.5.3/pasa_2.5.3.sif (built from the docker container docker://pasapipeline/pasapipeline:2.5.3). See the documentation at https://github.com/PASApipeline/PASApipeline/wiki . |
2 versions
|
| pboost | The boost module file defines the following environment variables: BOOST_DIR, BOOST_LIB, and BOOST_INC for the location of the boost distribution. Finally, it also modifies LD_LIBRARY_PATH to add the corresponding folder. Built with Intel compiler and Intel MPI 2017.0 |
3 versions
|
| pbsuite | This module loads the PATH and PYTHONPATH environment variables for pbsuite version 15.8.24 |
1 versions
|
| pcangsd | pcangsd: 1.10 Framework for analyzing low-depth (NGS) data in heterogeneous/structured populations using PCA MAKE SURE NO other of python is loaded than /usr/bin/python3.6 !!! python3 >>>import pcangsd Executable: pcangsd |
1 versions
|
| pdb-extract | This module loads the PATH and other environment variables for pdb_extract version 3.28. |
1 versions
|
| peakselector | PeakSelector |
1 versions
|
| pear | This package loads the environment to run pear (Paired-End reAd mergeR) version 0.9.6. To get syntaxon usage and options, enter 'pear' at the command line . |
1 versions
|
| peddy | This module loads the PATH and PYTHONPATH environment variables for peddy version 0.4.7. |
2 versions
|
| perl | Perl 5 is a highly capable, feature-rich programming language with over 27 years of development. |
4 versions
|
| perl-xml-simple | An API for simple XML files |
1 versions
|
| perturbo | This module loads the Perturbo environment |
2 versions
|
| petsc | PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. |
16 versions
|
| pgap | This module provides commands for the NCBI PGAP package based on the docker container described at https://github.com/ncbi/pgap . |
1 versions
|
| pgap2 | This module loads the PATH environment variable for pgap2 version 1.0.1. |
1 versions
|
| pgi | This module loads the Portland Group compiler path and environmental variables (v. 19.9). |
10 versions
|
| phase | This module sets the environment necessary to use phase 2.1.1 |
1 versions
|
| phast | This module sets the environment necessary to use phast |
2 versions
|
| phdf5 | This module loads: a. the PATH variable b. the LD_LIBRARY variable for Parallel HDF5 (v.1.8.19) |
4 versions
|
| phenix | This module loads the environment to run PHENIX |
7 versions
|
| phevor2 | This module sets the PATH and environment variable and loads a recent version of python 3 for for the phevor2 package. |
1 versions
|
| photoscan | This module sets the env. variables for Agisoft - Photoscan Name of the executable: photoscan.sh /metashape.sh Help: photoscan.sh --help metashape.sh --help |
4 versions
|
| phyml | This module provides the environment necessary to run phyml version 3.3.20190909. |
1 versions
|
| physpetree | This module sets up PhySpeTree container by calling the PhySpeTree command in the container Based on DockerHub container https://hub.docker.com/r/yangfangs/physpetree Run as "PhySpeTree arguments". |
1 versions
|
| phyx | Phyx: performs phylogenetics analyses on trees and sequences Executables are to be found in: /uufs/chpc.utah.edu/sys/installdir/r8/phyx/11092022/bin man pxrr |
4 versions
|
| picard | This module provides the environment necessary to run java code picard version 3.3.0 To see tools: java -jar $PICARD -h To use: java jvm-args -jar $PICARD PicardToolName OPTION1=value1.... requires (loaded as part of this module) jdk/1.8.0_rocky8 |
4 versions
|
| pigz | Module to set the env. variables for PIGZ (Parallel Pigz) a. pigz b. unpigz |
1 versions
|
| pilon | Software package for genome refinement. |
1 versions
|
| pixy | This module loads the PATH and PYTHONPATH environment variables for pixy version 1.2.3. |
1 versions
|
| plastid | This module loads the PATH and PYTHONPATH environment variables for plastid version 0.4.8. |
1 versions
|
| plink | This module sets the environment necessary to use plink 1.90 |
4 versions
|
| plinkseq | A library for the analysis of genetic variation data Binaries :: pseq, gcol, browser, behead, mm smp, tab2vcf, mongoose, pdas |
1 versions
|
| plumed | PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. |
76 versions
|
| pnetcdf | This module loads: a. the PATH variable b. the LD_LIBRARY variable for Parallel NetCDF library |
2 versions
|
| pod5 | POD5 is a file format for storing nanopore sequencing data in an easily accessible way. EXE :: pod5 depends on Python/3.11.3 To import the python pod5 module >>>import pod5 |
1 versions
|
| pomegranate | This module loads the anaconda environment for pomegranate version 0.14.3. |
1 versions
|
| poppler | Poppler is a PDF rendering library based on the xpdf-3.0 code base. |
1 versions
|
| positron | Positron - Data Science IDE |
1 versions
|
| postgresql | Postgresql 13.4 environment module |
6 versions
|
| prank | This module sets the environment necessary to use PRANK, version 170427 |
1 versions
|
| prest | This modulr sets the path for the 4.09 Prest-plus installation |
1 versions
|
| procheck | This module loads the PATH environment variable and creates aliases for programs in the procheck 3.5.4 and acqua 3.2 packages. |
1 versions
|
| prodigal | Module which sets the progidal env. variables prodigal -h |
1 versions
|
| proj | PROJ is a generic coordinate transformation software, that transforms geospatial coordinates from one coordinate reference system (CRS) to another. This includes cartographic projections as well as geodetic transformations. |
1 versions
|
| proj4 | PROJ is a generic coordinate transformation software, that transforms geospatial coordinates from one coordinate reference system (CRS) to another. This includes cartographic projections as well as geodetic transformations. The following ENV. variables will be set when loading this module: PROJ4 :: /uufs/chpc.utah.edu/sys/installdir/proj4/6.2.0 PROJ4_INCDIR :: /uufs/chpc.utah.edu/sys/installdir/proj4/6.2.0/include PROJ4_LIBDIR :: /uufs/chpc.utah.edu/sys/installdir/proj4/6.2.0/lib PKG_CONFIG_PATH :: /uufs/chpc.utah.edu/sys/installdir/proj4/6.2.0/lib/pkgconfig (Added on 02/11/2020) |
2 versions
|
| prokka | Prokka is a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. |
2 versions
|
| proteinmpnn | This module sets up the environment for ProteinMPNN from the David Baker lab. |
1 versions
|
| prothint | This module loads the PATH for prothint version 2.6.0. |
1 versions
|
| protobuf | This module loads the PATH variable for ProtocolBuffer (v.3.5.1) |
2 versions
|
| protomo | This sets up environment for protomo |
1 versions
|
| prottest | This module provides the environment necessary to run java program prottest version 3.4.2. To run: prottest3 URL: https://github.com/ddarriba/prottest3 |
1 versions
|
| pseudomarker | This module loads the PATH pseudomarker version 2.0. |
1 versions
|
| psi4conda | This module sets the PATH variable for psi4conda |
1 versions
|
| puffin | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
1 versions
|
| pugixml | Light-weight, simple, and fast XML parser for C++ with XPath support |
1 versions
|
| pvactools | pVACtools Executables: pvacseq, pvacbind, pvacfuse, pvacvector, pvacviz |
1 versions
|
| pvserver | ParaView is an open-source, multi-platform data analysis and visualization application. This package includes the Catalyst in-situ library for versions 5.7 and greater, othewise use the catalyst package. |
3 versions
|
| pwgui | This module loads the PATH environment variable for pwgui version 6.1. |
1 versions
|
| py-archspec | A library for detecting, labeling and reasoning about microarchitectures. |
1 versions
|
| py-cffi | Foreign Function Interface for Python calling C code |
2 versions
|
| py-cupy | CuPy is an open-source array library accelerated with NVIDIA CUDA. CuPy provides GPU accelerated computing with Python. CuPy uses CUDA-related libraries including cuBLAS, cuDNN, cuRand, cuSolver, cuSPARSE, cuFFT and NCCL to make full use of the GPU architecture. |
4 versions
|
| py-cython | The Cython compiler for writing C extensions for the Python language. |
17 versions
|
| py-dateutils | Various utilities for working with date and datetime objects. |
1 versions
|
| py-fastrlock | This is a C-level implementation of a fast, re-entrant, optimistic lock for CPython. |
1 versions
|
| py-fenics-basix | Python interface to Basix, a finite element definition and tabulation runtime library |
2 versions
|
| py-fenics-dolfinx | Python interface to the next generation FEniCS problem solving environment |
8 versions
|
| py-fenics-ffcx | Next generation FEniCS Form Compiler |
2 versions
|
| py-fenics-ufl | The Unified Form Language (UFL) is a domain specific language for declaration of finite element discretizations of variational forms. More precisely, it defines a flexible interface for choosing finite element spaces and defining expressions for weak forms in a notation close to mathematical notation. |
2 versions
|
| py-h5py | The h5py package provides both a high- and low-level interface to the HDF5 library from Python. |
2 versions
|
| py-hdfs | API and command line interface for HDFS |
1 versions
|
| py-imageio | Python library for reading and writing image data. Imageio is a Python library that provides an easy interface to read and write a wide range of image data, including animated images, video, volumetric data, and scientific formats. It is cross-platform, runs on Python 2.7 and 3.4+, and is easy to install. |
2 versions
|
| py-ipykernel | IPython Kernel for Jupyter |
4 versions
|
| py-ipython | IPython provides a rich toolkit to help you make the most out of using Python interactively. |
4 versions
|
| py-matplotlib | Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python. |
12 versions
|
| py-meshio | MeshIO is a Python library to read and write many mesh formats. |
4 versions
|
| py-meson-python | Meson Python build backend (PEP 517). |
1 versions
|
| py-mpi4py | This package provides Python bindings for the Message Passing Interface (MPI) standard. It is implemented on top of the MPI-1/MPI-2 specification and exposes an API which grounds on the standard MPI-2 C++ bindings. |
23 versions
|
| py-notebook | Jupyter Interactive Notebook |
4 versions
|
| py-numpy | NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, and useful linear algebra, Fourier transform, and random number capabilities |
31 versions
|
| py-pandas | pandas is a fast, powerful, flexible and easy to use open source data analysis and manipulation tool, built on top of the Python programming language. |
1 versions
|
| py-petsc4py | This package provides Python bindings for the PETSc package. |
4 versions
|
| py-pillow | Pillow is a fork of the Python Imaging Library (PIL). It adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities. |
5 versions
|
| py-pip | The PyPA recommended tool for installing Python packages. |
15 versions
|
| py-pooch | Pooch manages your Python library's sample data files: it automatically downloads and stores them in a local directory, with support for versioning and corruption checks. |
4 versions
|
| py-psycopg2 | Python interface to PostgreSQL databases |
1 versions
|
| py-pybind11 | pybind11 -- Seamless operability between C++11 and Python. pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code. Its goals and syntax are similar to the excellent Boost.Python library by David Abrahams: to minimize boilerplate code in traditional extension modules by inferring type information using compile-time introspection. |
1 versions
|
| py-pymol | PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is free to everyone! |
1 versions
|
| py-pytest | pytest: simple powerful testing with Python. |
4 versions
|
| py-pyvista | Easier Pythonic interface to VTK. |
10 versions
|
| py-requests | Python HTTP for Humans. |
1 versions
|
| py-scikit-learn | A set of python modules for machine learning and data mining. |
1 versions
|
| py-scipy | SciPy (pronounced "Sigh Pie") is a Scientific Library for Python. It provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization. |
12 versions
|
| py-scooby | A Great Dane turned Python environment detective. |
4 versions
|
| py-setuptools | A Python utility that aids in the process of downloading, building, upgrading, installing, and uninstalling Python packages. |
1 versions
|
| py-spyder | Scientific PYthon Development EnviRonment |
1 versions
|
| py-sqlalchemy | The Python SQL Toolkit and Object Relational Mapper |
1 versions
|
| pycles | This module loads the PATH and PYTHONPATH environment variables for pycles version 2018.10. (Pycles does not have official releases, so this version number is simply the date installed at CHPC. |
1 versions
|
| pyem | UCSF pyem Python programs for electron microscopy |
2 versions
|
| pymol | For best performance, run on a node with a graphics card, such as one of the frisco nodes. Then to start do 'vglrun -c proxy pymol' |
3 versions
|
| pypy | This module sets the environment necessary to use pypy 2.7 |
1 versions
|
| pyrosetta | PyRosetta - Python Bindings for the Rosetta library python3 >>>import pyrosetta >>>pyrosetta.init() |
1 versions
|
| python | This module loads the PATH & PYTHONHOME variable for Python 3.11.3 (Rocky8) Default: OMP_NUM_THREADS = 1 If you run a job with MORE than 1 SLURM task and use a package which depends on numpy and scipy, you should consider modifying the #OpenMP threads: export OMP_NUM_THREADS=$SLURM_NTASKS e.g.: # ----------- Start Code -------------------------------- from timeit import default_timer as timer import sys import os import numpy as np import numpy.random as rnd print(f'#OpenMP threads:{os.getenv("OMP_NUM_THREADS")}') start=timer() A = rnd.random((10000,10000)) B = rnd.random((10000,20000)) A@B end=timer() print(f" Elapsed time (s):{end-start:6.2f}") # ------------- End Code --------------------------------- |
42 versions
|
| qd | C++/Fortran-90 double-double and quad-double package. With modifications for easier integration with NJet. see http://crd- legacy.lbl.gov/~dhbailey/mpdist/ for authors page |
2 versions
|
| qemu | qemu-system-x86_64 -h |
2 versions
|
| qgis | Any help you want to display when running "module help module-name" |
3 versions
|
| qiime | This module sets a few ENVIRONMENTAL variables to useqiime and its assocated packages |
2 versions
|
| qiime2 | This module sets a few environment variables to use qiime2 and its assocated packages. |
3 versions
|
| qiime2amplicon | This module sets up the environment for the QIIME2 conda environment. Please note that this is the AMPLICON distribution. |
1 versions
|
| qt | Module to set the environmental variables for Qt (5.12.5) |
4 versions
|
| quantum-espresso | Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. |
26 versions
|
| quarto | Quarto :: Open-source scientific and technical publishing system built on Pandoc. The Quarto guide can be found at: https://quarto.org/docs/guide/ |
2 versions
|
| quast | This module loads the PATH and PYTHONPATH environment variables for quast version 5.2.0. Executables: {icarus,metaquast,quast-lg,quast}.py |
1 versions
|
| queue_gatk | This module provides the environment necessary to run java code Queue+GATK, verions 3.7. To run do $queue_gatk --help to see options. requires jdk/1.8.0_112 |
1 versions
|
| quip | QUIP - QUantum mechanics and Interatomic Potentials. Suite of tools to perform MD simulations. including ASE support. |
2 versions
|
| r | This module sets the ENVIRONMENTAL variables for R 4.5.2 i.e. "[Not] Part in a Rumble" (Released on 10/31/2025) What's new? see https://cran.r-project.org/doc/manuals/r-release/NEWS.html The R-build was performed using: gcc/13.3.0 (Support for C++, C++11, C++14, C++17, C++20, C++23) openblas v.0.3.30 (Threaded using OpenMP - vide infra) To modify #threads (default singlethreaded), you need to modify the value of the OMP_NUM_THREADS env. variable according to the #cores on the compute node, e.g.: export OMP_NUM_THREADS=12 (Bash) setenv OMP_NUM_THREADS 12 (Tcsh) The PDF-documentation is to be found in /uufs/chpc.utah.edu/sys/installdir/r8/R/4.5.2/doc It contains the following documents: fullrefman.pdf :: reference index (p. 3992) R-admin.pdf :: R Installation and Administration (p. 81) R-exts.pdf :: Writing R Extensions (p. 237) R-intro.pdf :: An Introduction to R (p. 104) R-ints.pdf :: R Internals (p. 73) R-lang.pdf :: R Language Definition (p. 60) R-data.pdf :: R Data Import/Export (p. 35) R-FAQ.pdf :: R FAQ (p. 51) Info on its shared R library can be found in the following way: pkg-config libR --path >> /uufs/chpc.utah.edu/sys/installdir/r8/R/4.5.2/lib64/pkgconfig/libR.pc pkg-config libR --libs >> -Wl,--export-dynamic -Wl,-rpath=/uufs/chpc.utah.edu/sys/installdir/r8/openblas/0.3.30-13.3.0g-gomp/lib -L/uufs/chpc.utah.edu/sys/installdir/r8/openblas/0.3.30-13.3.0g-gomp/lib -lopenblas -lm -lpthread -lgfortran -L/uufs/chpc.utah.edu/sys/installdir/r8/R/4.5.2/lib64/R/lib -lR pkg-config libR --cflags >> -I/uufs/chpc.utah.edu/sys/installdir/r8/R/4.5.2/lib64/R/include # Retrieve the content of the variables .. for var in rincludedir rlibdir rhome pcfiledir do pkg-config libR --variable=$var done /uufs/chpc.utah.edu/sys/installdir/r8/R/4.5.2/lib64/R/include /uufs/chpc.utah.edu/sys/installdir/r8/R/4.5.2/lib64/R/lib /uufs/chpc.utah.edu/sys/installdir/r8/R/4.5.2/lib64/R /uufs/chpc.utah.edu/sys/installdir/r8/R/4.5.2/lib64/pkgconfig |
26 versions
|
| r-applications | Loading this page makes all R (v. 3.6.2) container applications available |
1 versions
|
| racon | Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. |
2 versions
|
| radian | This module loads the anaconda environment for radian version 0.5.11 |
1 versions
|
| ragtag | RagTag: Tools for fast and flexible genome assembly scaffolding and improvement |
1 versions
|
| rapid | This module sets up the environment to run RAPID version 1.8.0 from docker://chdavid/rapid by aliasing the container call to the rapid executable. |
1 versions
|
| raxml | This module loads the PATH environment variable for raxml version 8.2.12. There are 3 versions of the raxml program: raxmlHPC Basic version of raxml, should run on any linux system. raxmlHPC-PTHREADS Same as above, with PTHREADS enabled. raxmlHPC-SSE3 SSE3 version - should run faster than basic version. raxmlHPC-PTHREADS-SSE3 Same as above, with PTHREADS enabled. raxmlHPC-AVX2 AVX2 version, which should run fastest on kingspeak and notchpeak nodes. raxmlHPC-PTHREADS-AVX2 Same as above, with PTHREADS enabled. |
1 versions
|
| raxml-ng | RAxML-NG is a phylogenetic tree inference tool which uses maximum- likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. RAxML-NG is a successor of RAxML (Stamatakis 2014) and leverages the highly optimized likelihood computation implemented in libpll (Flouri et al. 2014). |
2 versions
|
| rclone | This module provides the environment necessary to run rclone, a data transfer tool. To see options for use: rclone -h |
6 versions
|
| rdptools | This module provides the environment necessary to run java based RDPtools (Ribosomal Database Project Tools from MSU). To use java -jar $RDPTOOLS/<specific jarfile>. Tos see list of jar files, look at contents of $RDPTOOLS |
1 versions
|
| redis | Any help you want to display when running "module help module-name" |
1 versions
|
| redland | Redland RDF Library - librdf providing the RDF API and triple stores |
1 versions
|
| regenie | This module loads the PATH environment variable for regenie version 3.3. |
1 versions
|
| relion | Module file for relion, CPU accleration for AVX2 = ~24 core and newer CHPC servers |
48 versions
|
| remora | This module loads the PATH env. variable for REMORA 1.6 |
1 versions
|
| repeatmasker | RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. |
3 versions
|
| repeatscout | RepeatScout is a software tool for the de novo identication of repetitive element families in DNA sequences. |
1 versions
|
| reprise | REPrise: de novo interspersed repeat detection using inexact seeding |
1 versions
|
| resmap |
1 versions
|
|
| revbayes | Bayesian phylogenetic inference using probabilistic graphical models and an interpreted language. |
4 versions
|
| rfdiffusion | This module loads the environment and other modules for for rf_diffusion_all_atom, as of 2024-10-17. |
1 versions
|
| rheotool | The rheoTool toolbox, built on OpenFOAM 9 in an Ubuntu container |
1 versions
|
| rhessys | This module loads the environment variables for RHESSys version 7.4. To start RHESSys execute the command "grass64". |
3 versions
|
| riscv-gnu-toolchain | A cross-compilation tool for RISC-V. |
1 versions
|
| rmats-turbo | This module loads the PATH and other environment variables for rmats-turbo version 4.1.2. |
2 versions
|
| rnabloom | This module provides the environment necessary to run java code rnabloom, verions 2.0.1. To run the package execute "rnabloom". Requires jdk. |
1 versions
|
| rnafold | This module loads the PATH, LD_LIBRARY_PATH, PYTHONPATH, and PERL5LIB environment variables for RNAfold version 2.4.17. |
2 versions
|
| rnahybrid | This package loads the environment to run RNAhybrid, vesion 2.1.2 To get syntax on usage and options: RNAhybrid -h, RNAcalibrate -h, or RNAeffective -h . |
1 versions
|
| rocm | This module sets up environment for the AMD ROCm |
4 versions
|
| root | Modular scientific software toolkit |
4 versions
|
| rosetta | This module provides the environment necessary for Rosetta built with MPI and Tensorflow |
9 versions
|
| rosettafold2 | This module sets up the environment for RosettaFold2 from the David Baker lab. |
1 versions
|
| rsem | This module provides the environment necessary to run RSEM - RNA-Seq by Expectation-Maximixation" |
1 versions
|
| rsl | Radar Software Library to work with various input radar formats. Object-oriented library written in C This module: a. modifies the PATH variable b. sets the following Environmental Variables RSL_DIR /uufs/chpc.utah.edu/sys/installdir/rsl/1.49/ RSL_INCDIR /uufs/chpc.utah.edu/sys/installdir/rsl/1.49/include RSL_LIBDIR /uufs/chpc.utah.edu/sys/installdir/rsl/1.49/lib |
1 versions
|
| rsoft | This module sets the environment necessary to use RSoft 2024.09 |
2 versions
|
| rstudio | This module initializes the env. variables for RStudio 2024.12.0+467 What's new? https://blog.rstudio.com/ |
8 versions
|
| ruby | A dynamic, open source programming language with a focus on simplicity and productivity. |
2 versions
|
| rust | Rust: multi-paradigm programming language with focus on concurrency & safety The executables e.g. rustc, cargo, ... are found in: /uufs/chpc.utah.edu/sys/installdir/rust/1.87.0/bin |
4 versions
|
| rvic | This module sets the PATH environment variable and loads other required modules for the UW Hydro model RVIC. |
1 versions
|
| sac | This module sets up environment for Seismic Analysis Code (SAC) |
1 versions
|
| sagemath | This module sets up the environment to run sagemath version 9.4 Commands: sagemath :: To enter the singularity shell sage :: Sage executable as such jupyter :: Jupyter jupyter-notebook :: Jupyter notebook python :: Python executable |
2 versions
|
| salmon | This module sets the environment necessary to use salmon version 1.3.0 |
3 versions
|
| samba | samba -h |
1 versions
|
| sambamba | This module sets the PATH variable for sambamba Executable: sambamba |
1 versions
|
| samplot | This module loads the PATH and PYTHONPATH environment variables for samplot version 1.0.18 |
1 versions
|
| samtools | This module sets the environment necessary to use samtools |
5 versions
|
| samuel | This module sets the environment necessary to use samuel 15.01 scripts Use with /usr/bin/python; do 'ls /uufs/chpc.utah.edu/sys/installdir/samuel/sam/bin' to see list |
1 versions
|
| samviewer | This module sets up SamViewer 15.01 container running Ubuntu 16.06. |
1 versions
|
| sas | This module loads the environment to run SAS To start the SAS GUI: sas |
1 versions
|
| satscan | This module provides the environment necessary to run java code SatScan, version 9.6.1. |
1 versions
|
| sbg | This module provides the environment necessary to run sb from Seven Bridges Genomics Platform and sbg-uploader.sh . |
2 versions
|
| scafacos | ScaFaCoS is a library of scalable fast coulomb solvers. |
2 versions
|
| scala | This module loads the env. variables for Scala (v. 2.11.5) |
6 versions
|
| scanfold | Any help you want to display when running "module help module-name" |
1 versions
|
| scanpy | Module which sets the PATH variable for Scanpy v.1.9.1 Scanpy - Single-Cell Analysis in Python |
1 versions
|
| schlumberger | This module sets the variables for Schlumberger 2024.1 |
2 versions
|
| schrodinger | This script sets the environmental variables for the SCHRODINGER Suite. |
4 versions
|
| scipion | Module which sets the environmental variables for SCIPION v.3.1.0 i.e. based on python 3.11.4 |
2 versions
|
| scons | SCons Software building tool for software projects, similar to make or Cmake. www.scons.org |
4 versions
|
| scotch | Scotch is a software package for graph and mesh/hypergraph partitioning, graph clustering, and sparse matrix ordering. |
8 versions
|
| seekdeep | This module loads the environment and other modules for for seekdeep version 3.0.1. |
1 versions
|
| seismictools | Module which loads several INDEPENDENT tools used in seismology i.e. mseed2sac :: Convert miniSEED data to SAC sdrsplit :: Demultiplexication |
1 versions
|
| seismology | Setting the environemnt to run the "Computer Programs in Seismology" from the Saint Loius University Earthquake Center |
1 versions
|
| seissol | Module file for SeisSol |
2 versions
|
| sen2cor | This module sets a few environment variables to use sen2cor |
1 versions
|
| seqkit | seqkit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation EXECUTABLE: seqkit |
1 versions
|
| seqlinkage | This module sets up SEQLinkage container by aliasing the container call to the seqlink command Run as "seqlink arguments". |
1 versions
|
| seqmonk | This module loads SeqMonk 0.32.1 |
1 versions
|
| seqtk | This module sets the PATH variable for seqtk Executable: seqtk |
1 versions
|
| sextractor | This module sets the environment necessary to use Sextractor, Source-Extractor, version 2.25.0. It is a program that builds a catalog of objects from an astronomical image and is particularly oriented towards the reduction of large scale galaxy-survey data. |
1 versions
|
| sgs | This module provides the environment necessary to run java code sgs, version 3.5.0-11. Execute "sgs" to see options. This module also loads jdk/1.8.0_112. |
1 versions
|
| shapeit | Shapeit5 - successor of Shapeit4 The executables are: ligate_static : Ligate multiple phased BCF/VCF files into a single whole chromosome file. Typically run to ligate multiple chunks of phased common variants. phase_rare_static : Tool to phase rare variants onto a scaffold of common variants (output of phase_common / ligate) switch_static : Program to compute switch error rate and genotyping error rate given simulated or trio data. phase_common_static : Tool to phase common sites, typically SNP array data, or the first step of WES/WGS data phasing pipeline. This tool replaces SHAPEIT4. simulate_static xcftools_static : Program to convert between the various file formats used by shapeit5 [BCF from/to XCF]. |
3 versions
|
| shapelib | This module loads: a. the PATH variable for shapelib (v.1.3.0) |
1 versions
|
| shapeworks | This module sets the PATH variable for shapeworks/5.1 |
1 versions
|
| shellcheck | This module sets the environment necessary to use shellcheck |
1 versions
|
| shelxle | ShelXle - A cute graphical user interface for SHELXL |
1 versions
|
| shengbte | This module sets the environment to run the ShengBTE (https://bitbucket.org/sousaw/shengbte/src/master/) for serial mode: ShengBTE for parallel mode: mpirun -n 8 ShengBTE 2>BTE.err >BTE.out |
4 versions
|
| shortbred | This module sets up SHORTBred container. Based on DockerHub container biobakery/shortbre Run as "shortbred_identify.py arguments", or "shortbred_quantify.py arguments", Shell to the container is available as "startSHORTBred" |
1 versions
|
| shortstack | ShortStack small RNA alignment and analysis |
1 versions
|
| shotmap | This module sets the environment to run ShotMAP (Shotgun Metagenome Annotation Pipeline) |
1 versions
|
| sickle | This module provides the environment necessary to run sickle, a windowed adaptive trimming tool for FASTQ files To use: sickle se (for single end) or sickle pe (for paired end) |
1 versions
|
| sift4g | This module loads the PATH environment variable for sift4g commit id 8fd9f4 (last update on 11/03/2017; retrieved on 07/19/2023). run: sift4g --help |
1 versions
|
| signalp | This module sets environment variables and loads required modules for the SignalP signal peptide predicting software. |
2 versions
|
| sigprofiler | SigProfiler Bioinformatic Tools |
1 versions
|
| simba | This module sets a few environment variables to use simba assocated packages. (see also: https://simba-docs.readthedocs.io/en/latest/docs/intro/installation.html ) |
1 versions
|
| singularity | This module sets up singularity |
2 versions
|
| skytools | This module provides environment for Skytools pipelines based on Common Pipelines Library (CPL) |
1 versions
|
| slamdunk | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
1 versions
|
| slim | SLiM is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. Simulations are configured via the integrated Eidos scripting language that allows interactive control over practically every aspect of the simulated scenarios. The underlying individual-based simulation engine is highly optimized to enable modeling of entire chromosomes in large populations. We also provide a graphical user interface called SLiMgui on macOS, Linux, and Windows for easy simulation set-up, interactive runtime control, and dynamic visualization of simulation output. |
1 versions
|
| slurmjoblogquery | This module provides the environment necessary to run the python script to query the slurm job logs of the different clusters Requires python/3.9.7 |
1 versions
|
| smrttools | This module loads the SMRT Tools environment |
1 versions
|
| smufin | This module sets the environment to run SMuFin version 0.9.4. |
1 versions
|
| snakemake | This module loads the PATH and PYTHONPATH environment variables for snakemake version 9.3.3. This installation of snakemake includes the plugins for the slurm, aws-batch, azure-batch, and googlebatch executors, and the s3, azure, and gcs storage modules. |
11 versions
|
| snap | This module sets the PATH variable for snap/8.0 |
3 versions
|
| snappy | This module loads the PATH variable for Snappy (v. 1.1.2) |
1 versions
|
| snphylo | run: SNPhylo -H |
1 versions
|
| soapdenovo2 | This module provides the environment necessary to run soapdenovo2 version 2.04-r240. There are two executables, SOAPdenovo-63mer and SOAPdenovo-127mer. |
1 versions
|
| sod | Module which loads the environmental variables for the SOD package. The SOD package uses Java 1.7 or later. To invoke: sod |
1 versions
|
| solar | Module which sets the PATH variable for solar. |
1 versions
|
| solvate | Module which loads the environmental variables for the solvate package To invoke: solvate |
1 versions
|
| sortmerna | This package loads the environment to run sortmerna version 2.1 . To get syntax on usage and options, enter 'sortmerna -h' at the command line. |
2 versions
|
| spaceranger | Space Ranger is a set of analysis pipelines that process Visium data with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole transcriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen (FF) tissues. This package requires the user to accept a license and to download the tarball manually. Once downloaded, the file should be placed within a manual mirror or within the current directory. For instructions on making a manual mirror, see https://spack.readthedocs.io/en/latest/mirrors.html |
2 versions
|
| spack | This module loads the Spack package manager environment |
15 versions
|
| spade | SPADE is a software to explore various periodic repeat regions comprehensively from large genomic and protein data resources. |
1 versions
|
| spades | This module sets the environment necessary to use spades; runs with python3 in /usr/bin |
3 versions
|
| spark | Apache Spark is a fast and general-purpose cluster computing system. It provides high-level APIs in Java, Scala, Python and R, and an optimized engine that supports general execution graphs. It also supports a rich set of higher-level tools including Spark SQL for SQL and structured data processing, MLlib for machine learning, GraphX for graph processing, and Spark Streaming. To invoke interactively: pyspark (Python) spark-shell (Scala) sparkR (R) |
2 versions
|
| sparse | An open source sparse linear equation solver. |
2 versions
|
| specfem2d | SPECFEM2D simulates forward and adjoint seismic wave propagation in two-dimensional acoustic, (an)elastic, poroelastic or coupled acoustic-(an)elastic-poroelastic media, with Convolution PML absorbing conditions. |
1 versions
|
| specfem3d-cartesian | Program specfem3D from SPECFEM3D_GLOBE is a 3-D spectral-element solver for the Earth. It uses a mesh generated by program meshfem3D. |
2 versions
|
| specfem3d-globe | Program specfem3D from SPECFEM3D_GLOBE is a 3-D spectral-element solver for the Earth. It uses a mesh generated by program meshfem3D. |
4 versions
|
| spider | This module sets the PATH variable for spider version 26.04. Executable: spider |
1 versions
|
| spliceai | This module loads the PATH and PYTHONPATH environment variables for SpliceAI version 1.3.1. |
1 versions
|
| spring | This module sets the environment necessary to use spring |
1 versions
|
| sqlite | SQLite is a C-language library that implements a small, fast, self- contained, high-reliability, full-featured, SQL database engine. |
3 versions
|
| sra-toolkit | This module sets the environment necessary to use sra-toolkit |
6 versions
|
| stacks | Stacks: Software pipeline for building loci from short-read sequences |
1 versions
|
| star | Module to run STAR: Spliced Transcripts Alignment to a Reference to see options run STAR --help or STARlong --help. |
5 versions
|
| star-fusion | This module sets up the environment to run the deeplearning environment version 2024.2.0. |
1 versions
|
| starccm+ | This module sets the environment necessary to use star-ccm+ 13.06.011 |
2 versions
|
| starcd | This module sets the environment necessary to use star-cd 4.26 |
1 versions
|
| stata | Module which sets the PATH variable for STATA |
2 versions
|
| stringtie | This module sets the environment necessary to use stringtie |
1 versions
|
| structure | The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs. To invoke: structure |
1 versions
|
| su2 | SU2 is a suite of open-source software tools written in C++ for the numerical solution of partial differential equations (PDE) and performing PDE constrained optimization. |
7 versions
|
| subread | This module sets up the environment for programs in the subread package. |
2 versions
|
| subset-bam | subset-bam: tool to subset a 10x Genomics BAM file based on a tag subset-bam -h |
1 versions
|
| sundials | SUNDIALS (SUite of Nonlinear and DIfferential/ALgebraic equation Solvers) |
5 versions
|
| superlu-dist | A general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. |
2 versions
|
| sve | This module sets up sve container by aliasing the container run command to the sve command Based on DockerHub container https://hub.docker.com/r/wanpinglee/sve/ Run as "sve arguments". |
1 versions
|
| svn | This loads a modern version of the subversion repository system. To see help commands for svn, use "svn help". The commands provided by "svnadmin" can be used to initialize an empty repository. |
1 versions
|
| svtyper | This module loads the PATH and PYTHONPATH environment variables for svtyper version 0.7.0. |
1 versions
|
| swift | Swift language for parallel workflow development. http://swift-lang.org |
1 versions
|
| swig | SWIG is an interface compiler that connects programs written in C and C++ with scripting languages such as Perl, Python, Ruby, and Tcl. It works by taking the declarations found in C/C++ header files and using them to generate the wrapper code that scripting languages need to access the underlying C/C++ code. In addition, SWIG provides a variety of customization features that let you tailor the wrapping process to suit your application. |
1 versions
|
| syft | CLI tool and library for generating a Software Bill of Materials from container images and filesystems |
1 versions
|
| tassel | This module provides the environment necessary to run java code TASSEL 5.0. To run: start_tassel.pl |
1 versions
|
| taup | TauP: Seismic travel time calculator |
2 versions
|
| tbb | This module loads the Intel Threading Building Blocks |
1 versions
|
| tcoffee | This module loads the env. variables for T-Coffee, version 13.45.0 |
1 versions
|
| tcr-bert | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
1 versions
|
| tdep | Temperature Dependent Effective Potentials (TDEP) This package provides all the tools you need to build accurate model Hamiltonians for finite temperature lattice dynamics from first principles. In addition, there are codes to extract numerous physical properties from these model Hamiltonians, including but not limited to: a.Temperature dependent phonon frequencies b.Free energy including anharmonic contributions c.Phonon spectral functions, linewidths and shifts d.Lattice thermal conductivity |
2 versions
|
| tecplot | This module loads the environment to run tecplot To start the tecplot GUI: With a VGL capable grahics card do "vglrun -c proxy tec360" otherwise do "tec360" |
1 versions
|
| tensorflow | This module sets up tensorflow-gpu container by aliasing the container call to the tensorflow-gpu command Run as "tensorflow-gpu myprogram.py". |
2 versions
|
| tetools | This module sets up a TE Tools container, which includes commands RepeatModeler, RepeatMasker, BuildDatabase and runcoseg.pl. To run other commands, use syntax: TETools command_name command_arguments. |
1 versions
|
| tetranscripts | TEtranscripts: A package for including transposable elements in differential enrichment analysis of sequencing datasets Executables: TEtranscripts TEcount |
1 versions
|
| texinfo | Module to set the Env. Variables for Texinfo - GNU Documentation System |
1 versions
|
| texlive | This module sets up complete installation of TeXlive |
2 versions
|
| thirdorder | run: thirdorder_vasp.py sow|reap na nb nc cutoff[nm/-integer] |
2 versions
|
| tiledb | TileDB Library - Beyond tables and blobs |
1 versions
|
| tinker | This module sets the environment necessary to use tinker. version 8.2.1 |
1 versions
|
| tlusty | Tlusty: Package to accomplish a wide range of spectroscopic diagnostics Executable: tlusty200 To test benchmark: Testrun |
1 versions
|
| tmhmm | This loads the tmhmm. To use, type "tmhmm". |
1 versions
|
| topaz | This module loads the PATH and PYTHONPATH environment variables for topaz version 0.3.7. |
3 versions
|
| tophat | This module loads: a. the PATH variable for Tophat (v.2.1.1) |
1 versions
|
| tpepret | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
1 versions
|
| transrate | Transrate is a de-novo transcriptome assembly quality analysis package. |
1 versions
|
| trf | This module loads the PATH for trf version 4.09. |
2 versions
|
| trilinos | The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages. |
6 versions
|
| trim_galore | This module sets up the environment for trim_galore package. |
2 versions
|
| trimmomatic | This module provides the environment necessary to run trimmomatic version 0.39. To run trimmomatic either execute "trimmomatic arg1 arg2 ..." or java -jar $TRIMMOMATIC/trimmomatic-0.39.jar arg1 arg2 ...". |
1 versions
|
| trinity | This module provides the environment necessary to run trinity, version 2.14.0. To start: Trinity ; to start Inchworm: inchworm |
4 versions
|
| trust4 |
1 versions
|
|
| turbovnc | TurboVNC module |
2 versions
|
| ucscgenomeutilities | This module contains pre-built binaries for the UCSC Genome Browser Utilities. |
1 versions
|
| ucvm | The SCEC Unified Community Velocity Model (UCVM) software framework is a collection of software tools that provide a standard query interface to seismic velocity models. Once a seismic velocity model is registered into UCVM, it can be queried and combined with other velocity models through the UCVM software interface. |
1 versions
|
| udocker | This module sets up udocker |
4 versions
|
| udunits | This module loads: a. the PATH variable for udunits (v.2.2.25) |
1 versions
|
| umi-tools | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
1 versions
|
| unblur | Unblur is used to align the frames of movies recorded on an electron microscope to reduce image blurring due to beam-induced motion. It reads stacks of movies that are stored in MRC/CCP4 format. |
1 versions
|
| unrar | The UnRar package contains a RAR extraction utility used for extracting files from RAR archives. To see all the flags: unrar |
2 versions
|
| upc | Berkeley Unified Parallel C |
3 versions
|
| upcxx | Berkeley Unified Parallel C++ |
3 versions
|
| uprof | This module loads the AMD uprof environment |
1 versions
|
| usearch | Usearch is a genomic sequence analysis tool program used with qiime and linked to name usearch61 |
2 versions
|
| usf | This package loads the environment to run usf (Uppsala Software Factory) tools Note - that about half of the tools did not run, so I removed them form the installation |
1 versions
|
| valgrind | An instrumentation framework for building dynamic analysis. 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. Valgrind is Open Source / Free Software, and is freely available under the GNU General Public License, version 2. |
1 versions
|
| vamb | This module loads the PATH and PYTHONPATH environment variables for vamb version 3.0.3. |
1 versions
|
| vapor | This module loads environment for Vapor (v.2.6.0) |
3 versions
|
| variantdetective | This module sets the PATH variable for VariantDetective. Run as variantdetective |
1 versions
|
| varnet | This module loads the PATH and PYTHONPATH environment variables for varnet version 1.1.0. |
1 versions
|
| vasp | VASP 5.4.4 Compiled with Intel 2017.4.196 & Intel MPI 2017.4.196 |
33 versions
|
| vcf-kit | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
1 versions
|
| vcf2tsvpy | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
1 versions
|
| vcfdist | This module sets the environment necessary to use vcfdist v.2.6.1 |
1 versions
|
| vcflib |
1 versions
|
|
| vcftools | This package loads the environment to run vcftools, version 0.1.15-6 To run vcftools; see other commands in /uufs/chpc.utah.edu/sys/installdir/vcftools/0.1.15-6/bin |
2 versions
|
| vdjtools | VDJtools is a comprehensive analysis framework for T-cell and B-cell repertoire sequencing data. Usage: vdjtools vdjtools CalcBasicStats -h ... |
1 versions
|
| velocyto | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
1 versions
|
| vep | This module sets up the environment to run VEP version 104.2 from docker://ensemblorg/ensembl-vep by aliasing the container call to the vep executable. |
2 versions
|
| vic | This module sets the PATH environment variable and loads other required modules for the UW Hydro model VIC. |
2 versions
|
| vim | This module provides the environment necessary to run vim. To see options for use: 'man vim' |
2 versions
|
| viralconsensus | This module loads the PATH environment variable for ViralConsensus version 0.0.5. The executable program is named "viral_consensus". |
1 versions
|
| visit | VisIt visualization framework This module loads the VisIt visualization framework. Version 3.2.2 |
3 versions
|
| visualsfm | This module provides the environment necessary to run VisualSFM version0.5.26. To start use "VisualSFM" |
1 versions
|
| vmd | This package loads the VMD molecular viewer. To start the program, use 'vmd' at the command line. The following env. variables have been set: PATH :: /uufs/chpc.utah.edu/sys/installdir/vmd/1.9.3/bin VMD_PLUGIN_INCDIR :: /uufs/chpc.utah.edu/sys/installdir/vmd/1.9.3/lib/vmd/plugins/include VMD_PLUGIN_LIBDIR :: /uufs/chpc.utah.edu/sys/installdir/vmd/1.9.3/lib/vmd/plugins/LINUXAMD64 |
3 versions
|
| voropp | Voro++ is a open source software library for the computation of the Voronoi diagram, a widely-used tessellation that has applications in many scientific fields. |
6 versions
|
| vpl | This module loads the Intel Video Processing Library |
1 versions
|
| vscode | This module initializes the env. variables for VSCode 1.96.0 |
2 versions
|
| vsearch | This module sets the PATH variable for vsearch Executable: vsearch |
1 versions
|
| vtk | The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. |
11 versions
|
| vtune | This module loads the VTUNE environment |
5 versions
|
| wannier90 | Wannier90 calculates maximally-localised Wannier functions (MLWFs). Wannier90 is released under the GNU General Public License. |
13 versions
|
| wanniertools | WannierTools: An open-source software package for novel topological materials. |
1 versions
|
| warp | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
1 versions
|
| wasp | This module sets up EPA WASP |
1 versions
|
| wdfs | This module sets a few ENVIRONMENTAL variables for Wdfs |
1 versions
|
| weka | This module sets the PATH variable for weka (v.3.8.1) The weka.jar file is to be found in /uufs/chpc.utah.edu/sys/installdir/weka/3.8.1/weka.jar |
3 versions
|
| westpa | Module which sets the PATH variable for user instaled miniconda To check the available packages: conda list |
1 versions
|
| wf_human_variation | This module loads the PATH environment variable and sets up the environment for wf_human_variation workflow version 1.9.2 from Oxford Nanopore. |
1 versions
|
| wgrib | This loads the wgrib utility. To use, type "wgrib". |
1 versions
|
| wgrib2 | This loads the wgrib2 utility. To use, type "wgrib2". |
3 versions
|
| whatshap | Module which sets the PATH variable for WhatsHap (conda env) To check help page: whatshap --help |
1 versions
|
| wi4mpi | WI4MPI: Wrapper Interface For MPI performing a light translation between MPI constants and MPI objects from an MPI implementation to another one |
3 versions
|
| wien2k | This module provides the environment necessary to run Wien2K version 14.2 |
1 versions
|
| wrf | The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications. |
4 versions
|
| xcrysden | Any help you want to display when running "module help module-name" |
1 versions
|
| xds |
1 versions
|
|
| xgboost | XGBOOST: Extreme Gradient Boosting: Open-source machine learning (ML) algorithm and library that trains gradient boosted models. Used for regression, classification, and ranking tasks on tabular datasets. Compiled with support for: a.OpenMP b.GPUs: 1.NCCL (i.e. multi-GPUs) 2.Optimized for the following (NVIDIA) GPU architectures: 5.2, 6.0, 6.1, 7.0, 7.5, 8.0,8.6, 8.9, 9.0 |
1 versions
|
| xmmsas | This module loads the XMM-Newton SAS environment |
1 versions
|
| xsite | xsite : Hydraulic Fracture Simulation of 3D Fracture Networks |
1 versions
|
| xtb | xtb - Semi-empirical Tight-Binding Program |
3 versions
|
| yambo | Module file for YAMBO |
2 versions
|
| yaml-cpp | A YAML parser and emitter in C++ |
5 versions
|
| yorick | This module sets the environment for yorick version 2.2.04: - Yorick is located in /uufs/chpc.utah.edu/sys/installdir/yorick/2.2.04/bin and that directory is added to your PATH. |
1 versions
|
| zig | Zig Programming Language Imperative, general-purpose, statically typed, compiled system programming language |
1 versions
|
| zlib | A free, general-purpose, legally unencumbered lossless data-compression library. |
19 versions
|