302 container modules.
github container description aliases
GITHUB adminer Database management in a single PHP file.
GITHUB bids/aa BIDS App containing an instance of the Automatic Analysis. (https://github.com/BIDS-Apps/aa)
GITHUB bids/baracus Brain-Age Regression Analysis and Computation Utility Software (https://github.com/BIDS-Apps/baracus)
GITHUB bids/brainiak-srm Shared Response Model (SRM) from the Brain Imaging Analysis Kit (BrainIAK) (https://github.com/BIDS-Apps/brainiak-srm)
GITHUB bids/brainsautoworkup A BIDS App for running BRAINSAutoWorkup (https://github.com/BIDS-Apps/BRAINSAutoworkup)
GITHUB bids/broccoli BROCCOLI is a software for analysis of fMRI (functional magnetic resonance imaging) data and is written in OpenCL (Open Computing Language). (https://github.com/BIDS-Apps/BROCCOLI)
GITHUB bids/freesurfer Surface reconstruction using Freesurfer
GITHUB bids/hcppipelines BIDS-ified HPC Piplines to process MRI data for the Human Connectome Project (https://github.com/BIDS-Apps/HCPPipelines)
GITHUB bids/matlab-compiler-runtime Base image with Matlab compiler runtime (https://github.com/BIDS-Apps/matlab-compiler-runtime)
GITHUB bids/mrtrix3_connectome Generation and subsequent group analysis of structural connectomes generated from diffusion MRI data (via the MRtrix3 software package). https://github.com/BIDS-Apps/MRtrix3_connectome
GITHUB bids/niak The neuroimaging analysis kit. Pipeline for preprocessing of fMRI and structural MRI scans http://niak.simexp-lab.org/ (https://github.com/BIDS-Apps/niak)
GITHUB bids/pymvpa Take fMRI data and generates ROI based MultiVariate Pattern Analysis (MVPA) outputs (https://github.com/BIDS-Apps/PyMVPA)
GITHUB bids/rshrf Resting state HRF estimation and deconvolution (https://github.com/BIDS-Apps/rsHRF) rsHRF
GITHUB bids/spm The implementation of the theoretical concepts of Statistical Parametric Mapping in a complete analysis package. spm12
GITHUB bids/tracula Implements Freesurfer's TRACULA (TRActs Constrained by UnderLying Anatomy) tool for cross-sectional as well as longitudinal (multi session) input data (https://github.com/BIDS-Apps/tracula)
GITHUB bids/validator A validator for BIDS (Brain Imaging Data Structure) datasets. bids-validator
GITHUB biocontainers/abyss A de novo, parallel, paired-end sequence assembler that is designed for short reads. See https://www.bcgsc.ca/resources/software/abyss. abyss-fixmate, abyss-pe
GITHUB biocontainers/bamtools BamTools is a toolkit for handling BAM files. bamtools
GITHUB biocontainers/bcftools BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. bcftools
GITHUB biocontainers/bedtools a powerful toolset for genome arithmetic bedtools
GITHUB biocontainers/bowtie2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. bowtie2, bowtie2-inspect, bowtie2-build
GITHUB biocontainers/bwa BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. bwa
GITHUB biocontainers/emboss Free Open Source software analysis package which covers several molecular biology tools. embossdata, embossupdate, embossversion, emma, emowse, em_pscan, em_cons
GITHUB biocontainers/fastqc A quality control tool for high throughput sequence data.
GITHUB biocontainers/picard-tools The Picard command-line tools are packaged as executable jar files.
GITHUB biocontainers/picard Java CLI tools for manipulating HTS data and formats picard
GITHUB biocontainers/plink1.9 An update to PLINK, a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. plink
GITHUB biocontainers/samtools Samtools is a suite of programs for interacting with high-throughput sequencing data. samtools
GITHUB biocontainers/tabix Fast retrieval of sequence features from generic TAB-delimited files. tabix
GITHUB biocontainers/talon Mailgun library to extract message quotations and signatures. talon, talon_create_GTF, talon_fetch_reads, talon_filter_transcripts, talon_generate_report, talon_initialize_database, talon_get_sjs, talon_label_reads, talon_reformat_gtf, talon_summarize, talon_abundance
GITHUB biocontainers/tpp The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC. config_data, json_xs, lwp-download, lwp-dump, lwp-mirror, lwp-request
GITHUB biocontainers/vcftools VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. vcftools
GITHUB consul Consul is a datacenter runtime that provides service discovery, configuration, and orchestration. consul
GITHUB couchdb CouchDB is a database that uses JSON for documents, an HTTP API, & JavaScript/declarative indexing. couchdb, couchdb.cmd, couchjs, remsh
GITHUB elasticsearch Elasticsearch is a powerful open source search and analytics engine that makes data easy to explore. elasticsearch, elasticsearch-certgen, elasticsearch-certutil, elasticsearch-cli, elasticsearch-croneval, elasticsearch-env, elasticsearch-env-from-file, elasticsearch-keystore, elasticsearch-migrate, elasticsearch-node, elasticsearch-plugin, elasticsearch-saml-metadata, elasticsearch-setup-passwords, elasticsearch-shard, elasticsearch-sql-cli, elasticsearch-sql-cli-7.12.0.jar, elasticsearch-syskeygen, elasticsearch-users
GITHUB ghcr.io/autamus/abi-dumper ABI Dumper is a tool for dumping ABI information of an ELF object containing DWARF debug info. abi-dumper
GITHUB ghcr.io/autamus/abyss ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. abyss-align, abyss-bloom, abyss-bloom-dbg, abyss-bloom-dist.mk, abyss-bowtie, abyss-bowtie2, abyss-bwa, abyss-bwamem, abyss-bwasw, abyss-db-csv, abyss-db-txt, abyss-dida, abyss-fac, abyss-fatoagp, abyss-filtergraph, abyss-fixmate, abyss-fixmate-ssq, abyss-gapfill, abyss-gc, abyss-index, abyss-junction, abyss-kaligner, abyss-layout, abyss-longseqdist, abyss-map, abyss-map-ssq, abyss-mergepairs, abyss-overlap, abyss-paired-dbg, abyss-paired-dbg-mpi, abyss-pe, abyss-samtoafg, abyss-scaffold, abyss-sealer, abyss-stack-size, abyss-tabtomd, abyss-todot, abyss-tofastq
GITHUB ghcr.io/autamus/accumulo Apache Accumulo is a sorted, distributed key/value store that provides robust, scalable data storage and retrieval.
GITHUB ghcr.io/autamus/addrwatch addrwatch is a similar software to arpwatch. It main purpose is to monitor network and log ethernet/ip pairings. addrwatch, addrwatch_stdout, addrwatch_syslog
GITHUB ghcr.io/autamus/adios The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists to describe the data in their code that may need to be written, read, or processed outside of the running simulation. adios_config, adios_lint, adios_list_methods, adios_list_methods_nompi, adios_list_methods_readonly, adios_list_methods_readonly_nompi
GITHUB ghcr.io/autamus/adios2 The Adaptable Input Output System version 2, developed in the Exascale Computing Program adios2-config, adios2_deactivate_bp, adios2_iotest, adios2_reorganize, adios2_reorganize_mpi
GITHUB ghcr.io/autamus/admixtools ADMIXTOOLS is a collection of programs which use genetic data to infer how populations are related to one another. convertf, dowtjack, expfit.sh, gcount, grabpars, gsl-config, gsl-histogram, gsl-randist, jackdiff, kimf, mergeit, mkpretty, qp3Pop, qp4diff, qpAdm, qpBound, qpDpart, qpDstat, qpF4ratio, qpGraph, qpWave, qpdslow, qpff3base, qpfmv, qpfstats, qpreroot, rexpfit.r, rolloff, rolloffp, simpjack2, twtable, wtjack.pl
GITHUB ghcr.io/autamus/advancecomp AdvanceCOMP is a set of cross-platform command line data (re-)compression tools. advdef, advmng, advpng, advzip
GITHUB ghcr.io/autamus/alan A simple in-terminal alignment viewer. alan
GITHUB ghcr.io/autamus/alps Algorithms and Libraries for Physics Simulations. alpspython
GITHUB ghcr.io/autamus/amrex AMReX is a publicly available software framework designed for building massively parallel block- structured adaptive mesh refinement (AMR) applications.
GITHUB ghcr.io/autamus/angsd ANGSD is a software for analyzing next generation sequencing data. angsd
GITHUB ghcr.io/autamus/arborx ArborX is a performance-portable library for geometric search
GITHUB ghcr.io/autamus/argobots A lightweight runtime system that supports integrated computation and data movement with massive concurrency.
GITHUB ghcr.io/autamus/aria2 aria2 is a lightweight multi-protocol & multi-source command-line download utility. aria2c
GITHUB ghcr.io/autamus/ascent An open source many-core capable lightweight in situ visualization and analysis infrastructure for multi-physics HPC simulations.
GITHUB ghcr.io/autamus/astral ASTRAL is a tool for estimating an unrooted species tree given a set of unrooted gene trees. astral
GITHUB ghcr.io/autamus/bart BART: Toolbox for Computational Magnetic Resonance Imaging bart, bartview
GITHUB ghcr.io/autamus/bbmap A suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.
GITHUB ghcr.io/autamus/bcftools BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. bcftools
GITHUB ghcr.io/autamus/beast2 BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. beast, beasti, beauti, densitree, treeannotator
GITHUB ghcr.io/autamus/bedops BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. bam2bed, bam2bed_gnuParallel, bam2bed_sge, bam2bed_slurm, bam2starch, bam2starch_gnuParallel, bam2starch_sge, bam2starch_slurm, bedextract, bedmap, bedops, closest-features, convert2bed, gff2bed, gff2starch, gtf2bed, gtf2starch, gvf2bed, gvf2starch, psl2bed, psl2starch, rmsk2bed, rmsk2starch, sam2bed, sam2starch, sort-bed, starch, starch-diff, starchcat, starchcluster_gnuParallel, starchcluster_sge, starchcluster_slurm, starchstrip, unstarch, update-sort-bed-migrate-candidates, update-sort-bed-slurm, update-sort-bed-starch-slurm, vcf2bed, vcf2starch, wig2bed, wig2starch
GITHUB ghcr.io/autamus/bedtools2 The swiss army knife for genome arithmetic annotateBed, bamToBed, bed12ToBed6, bedToBam, bedToIgv, bedpeToBam, bedtools, closestBed, clusterBed, complementBed, coverageBed, fastaFromBed, flankBed, genomeCoverageBed, intersectBed, linksBed, mapBed, maskFastaFromBed, mergeBed, multiIntersectBed, nucBed, pairToBed, randomBed, shiftBed, shuffleBed, slopBed, sortBed, subtractBed, unionBedGraphs, windowBed
GITHUB ghcr.io/autamus/bismark Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. bismark, bismark_genome_preparation, bismark_methylation_extractor, bismark2bedGraph, bismark2report, bismark2summary
GITHUB ghcr.io/autamus/bolt BOLT targets a high-performing OpenMP implementation, especially specialized for fine-grain parallelism.
GITHUB ghcr.io/autamus/boost The Boost project provides free peer-reviewed portable C++ source libraries.
GITHUB ghcr.io/autamus/bowtie2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. bowtie2, bowtie2-align-l, bowtie2-align-s, bowtie2-build, bowtie2-build-l, bowtie2-build-s, bowtie2-inspect, bowtie2-inspect-l, bowtie2-inspect-s
GITHUB ghcr.io/autamus/bracken Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
GITHUB ghcr.io/autamus/bwa BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. bwa
GITHUB ghcr.io/autamus/cabana The Exascale Co-Design Center for Particle Applications Toolkit
GITHUB ghcr.io/autamus/caliper Caliper is a program instrumentation and performance measurement framework. cali-query, cali-stat
GITHUB ghcr.io/autamus/cantera Cantera is an open-source collection of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and transport processes.
GITHUB ghcr.io/autamus/cctools The Cooperative Computing Tools (CCTools) are a collection of programs that enable large scale distributed computing on systems such as clusters, clouds, and grids. c_rehash, captoinfo, catalog_query, catalog_server, catalog_update, ccache-swig, cctools_gpu_autodetect, chirp, chirp_audit_cluster, chirp_benchmark, chirp_distribute, chirp_fuse, chirp_get, chirp_put, chirp_server, chirp_server_hdfs, chirp_status, chirp_stream_files, chroot_package_run, clear, condor_submit_makeflow, condor_submit_workers, confuga_adm, corelist, cpan, cpanm
GITHUB ghcr.io/autamus/cdo CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. cdo
GITHUB ghcr.io/autamus/cfitsio CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.
GITHUB ghcr.io/autamus/circos Circos is a software package for visualizing data and information. circos
GITHUB ghcr.io/autamus/clhep CLHEP is a C++ library that provides utility classes for general numerical programming, vector arithmetic, geometry, pseudorandom number generation, and linear algebra, specifically targeted for high energy physics simulation and analysis software. Cast-config, Evaluator-config, Exceptions-config, GenericFunctions-config, Geometry-config, Matrix-config, Random-config, RandomObjects-config, RefCount-config, Units-config, Utility-config, Vector-config, clhep-config
GITHUB ghcr.io/autamus/clingo An ASP system to ground and solve logic programs. clingo, gringo
GITHUB ghcr.io/autamus/cloc cloc is a command line program that takes file, directory, and/or archive names as inputs. cloc
GITHUB ghcr.io/autamus/conduit Conduit is an open source project from Lawrence Livermore National Laboratory that provides an intuitive model for describing hierarchical scientific data in C++, C, Fortran, and Python. conduit_blueprint_verify, conduit_relay_entangle.py, conduit_relay_io_convert, conduit_relay_io_ls, conduit_relay_node_viewer, conduit_staging, conduit_staging.sh
GITHUB ghcr.io/autamus/corset Corset is a command-line program to go from a de novo transcriptome assembly to gene-level counts. corset, corset_fasta_ID_changer
GITHUB ghcr.io/autamus/cowsay What does the cow say? cowsay
GITHUB ghcr.io/autamus/cufflinks Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. cuffcompare, cuffdiff, cufflinks, cuffmerge, cuffnorm, cuffquant
GITHUB ghcr.io/autamus/curl cURL is a computer software project providing a library and command-line tool for transferring data using various network protocols. The name stands for 'Client URL', which was first released in 1997. c_rehash, curl, curl-config
GITHUB ghcr.io/autamus/dakota The Dakota project delivers both state-of-the-art research and robust, usable software for optimization and UQ. Broadly, the Dakota software's advanced parametric analyses enable design exploration, model calibration, risk analysis, and quantification of margins and uncertainty with computational models. dakota, dakota_library_mode, dakota_library_split, dakota_order_input, dakota_restart_util
GITHUB ghcr.io/autamus/datatransferkit DataTransferKit is an open-source software library of parallel solution transfer services for multiphysics simulations
GITHUB ghcr.io/autamus/diamond A sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. diamond
GITHUB ghcr.io/autamus/dyninst DyninstAPI - Tools for binary instrumentation, analysis, and modification.
GITHUB ghcr.io/autamus/eagle Explicit Alternative Genome Likelihood Evaluator eagle, eagle-nm, eagle-rc
GITHUB ghcr.io/autamus/ed GNU ed is a line-oriented text editor used to create, display, modify and otherwise manipulate text files, both interactively and via shell scripts https://www.gnu.org/software/ed. ed, red
GITHUB ghcr.io/autamus/emacs The Emacs programmable text editor. https://www.gnu.org/software/emacs ebrowse, emacs, emacsclient, etags
GITHUB ghcr.io/autamus/faodel Flexible, Asynchronous, Object Data-Exchange Libraries faodel
GITHUB ghcr.io/autamus/fastqc A quality control tool for high throughput sequence data. fastqc
GITHUB ghcr.io/autamus/ffmpeg FFmpeg is a free and open-source software project consisting of a large suite of libraries and programs for handling video, audio, and other multimedia files and streams. ffmpeg, ffprobe
GITHUB ghcr.io/autamus/flit Floating-point Litmus Tests (FLiT) is a C++ test infrastructure for detecting variability in floating-point code caused by variations in compiler code generation, hardware and execution environments. flit
GITHUB ghcr.io/autamus/fraggenescan An application for finding (fragmented) genes in short reads.
GITHUB ghcr.io/autamus/gasnet GASNet is a language-independent, networking middleware layer that provides network-independent, high-performance communication primitives including Remote Memory Access (RMA) and Active Messages (AM). gasnet_trace, gasnet_trace.pl
GITHUB ghcr.io/autamus/gatk GATK (pronounced 'Gee-ay-tee-kay', not 'Gat-kay'), stands for GenomeAnalysisToolkit. It is a collection of command-line tools for analyzing high-throughput sequencing data with a primary focus on variant discovery. gatk
GITHUB ghcr.io/autamus/gawk gawk is the GNU implementation of awk. The awk utility interprets a special-purpose programming language that makes it possible to handle simple data-reformatting jobs with just a few lines of code. https://www.gnu.org/software/gawk/ gawk
GITHUB ghcr.io/autamus/gcc The GNU Compiler Collection c++, cpp, g++, gcc, gcc-ar, gcc-nm, gcc-ranlib, gcov, gcov-dump, gcov-tool, gfortran, zstd
GITHUB ghcr.io/autamus/gdal GDAL is a translator library for raster and vector geospatial data formats that is released under an X/MIT style Open Source License by the Open Source Geospatial Foundation. gdal-config, gdal_contour, gdal_create, gdal_grid, gdal_rasterize, gdal_translate, gdal_viewshed, gdaladdo, gdalbuildvrt, gdaldem, gdalenhance, gdalinfo, gdallocationinfo, gdalmanage, gdalmdiminfo, gdalmdimtranslate, gdalsrsinfo, gdaltindex, gdaltransform, gdalwarp
GITHUB ghcr.io/autamus/geant4 Geant4 is a platform for the simulation of the passage of particles through matter using Monte Carlo methods. Cast-config, CreateDOMDocument, DOMCount, DOMPrint, EnumVal, Evaluator-config, Exceptions-config, GenericFunctions-config, Geometry-config, Matrix-config, MemParse, PParse, PSVIWriter, Random-config, RandomObjects-config, Redirect, RefCount-config, SAX2Count, SAX2Print, SAXCount, SAXPrint, SCMPrint, SEnumVal, StdInParse, Units-config, Utility-config, Vector-config, XInclude, geant4-config, geant4.csh, geant4.sh
GITHUB ghcr.io/autamus/geos GEOS is a C++11 library for performing operations on two-dimensional vector geometries. geos-config
GITHUB ghcr.io/autamus/ginkgo High-performance linear algebra library for manycore systems, with a focus on sparse solution of linear systems.
GITHUB ghcr.io/autamus/git Git is software for tracking changes in any set of files, usually used for coordinating work among programmers collaboratively developing source code during software development. Its goals include speed, data integrity, and support for distributed, non-linear workflows. git, git-cvsserver, git-receive-pack, git-shell, git-upload-archive, git-upload-pack
GITHUB ghcr.io/autamus/glpk The GLPK package is a set of routines written in ANSI C and organized in the form of a callable library. This package is intended for solving large-scale linear programming (LP), mixed integer linear programming (MIP), and other related problems. glpsol
GITHUB ghcr.io/autamus/gmp GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers. curl
GITHUB ghcr.io/autamus/gnuplot Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. gnuplot
GITHUB ghcr.io/autamus/gotcha C software library for shared library function wrapping, enables tools to intercept calls into shared libraries
GITHUB ghcr.io/autamus/graphviz Graphviz is open source graph visualization software. gc, gml2gv, graphml2gv, gv2gml, gv2gxl, gvcolor, gvgen, gvmap, gvmap.sh, gvpack, gvpr, gxl2dot, gxl2gv
GITHUB ghcr.io/autamus/grass GRASS GIS (https://grass.osgeo.org/) is a Geographic Information System used for geospatial data management and analysis, image processing, graphics/map production, spatial modeling, and visualization. grass78
GITHUB ghcr.io/autamus/gromacs A versatile package to perform molecular dynamics.
GITHUB ghcr.io/autamus/gsl The GNU Scientific Library. gsl-config, gsl-histogram, gsl-randist
GITHUB ghcr.io/autamus/hdf5 HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. h5clear, h5copy, h5debug, h5diff, h5dump, h5format_convert, h5import, h5jam, h5ls, h5mkgrp, h5pcc, h5perf, h5perf_serial, h5redeploy, h5repack, h5repart, h5stat, h5unjam
GITHUB ghcr.io/autamus/heaptrack Heaptrack traces all memory allocations and annotates these events with stack traces. heaptrack, heaptrack_print
GITHUB ghcr.io/autamus/hisat2 HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. hisat2, hisat2-align-l, hisat2-align-s, hisat2-build, hisat2-build-l, hisat2-build-s, hisat2-inspect, hisat2-inspect-l, hisat2-inspect-s, hisat2_extract_exons.py, hisat2_extract_snps_haplotypes_UCSC.py, hisat2_extract_snps_haplotypes_VCF.py, hisat2_extract_splice_sites.py, hisat2_read_statistics.py, hisat2_simulate_reads.py, hisatgenotype.py, hisatgenotype_build_genome.py, hisatgenotype_extract_reads.py, hisatgenotype_extract_vars.py, hisatgenotype_hla_cyp.py, hisatgenotype_locus.py
GITHUB ghcr.io/autamus/hmmer HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. hmmalign, hmmbuild, hmmconvert, hmmemit, hmmfetch, hmmlogo, hmmpgmd, hmmpgmd_shard, hmmpress, hmmscan, hmmsearch, hmmsim, hmmstat
GITHUB ghcr.io/autamus/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. hello, hpclink, hpcprof, hpcrun, hpcstruct, hpcviewer
GITHUB ghcr.io/autamus/hpx C++ runtime system for parallel and distributed applications. hpxcxx, hpxrun.py
GITHUB ghcr.io/autamus/htop htop is an interactive text-mode process viewer for Unix systems. https://github.com/hishamhm/htop htop
GITHUB ghcr.io/autamus/htslib A C library for reading/writing high-throughput sequencing data. htsfile
GITHUB ghcr.io/autamus/hypre A library of high performance preconditioners and solvers featuring multigrid methods for the solution of large, sparse linear systems of equations on massively parallel computers.
GITHUB ghcr.io/autamus/igraph igraph is a library collection for creating and manipulating graphs and analyzing networks. It is written in C and also exists as Python and R packages.
GITHUB ghcr.io/autamus/intel-mkl Intel oneAPI Math Kernel Library, formerly just Intel Math Kernel Library, is a library of optimized math routines for science, engineering, and financial applications.
GITHUB ghcr.io/autamus/ior IOR is a parallel IO benchmark that can be used to test the performance of parallel storage systems using various interfaces and access patterns. ior
GITHUB ghcr.io/autamus/iq-tree IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. iq-tree2
GITHUB ghcr.io/autamus/jags Just Another Gibbs Sampler. A program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation. jags
GITHUB ghcr.io/autamus/jasper JasPer is a collection of software (i.e., a library and application programs) for the coding and manipulation of images. jasper, jpegtran
GITHUB ghcr.io/autamus/julia Julia is a high-level, high-performance, dynamic programming language. julia
GITHUB ghcr.io/autamus/kallisto kallisto is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. kallisto
GITHUB ghcr.io/autamus/kraken2 Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. kraken2, kraken2-build, kraken2-inspect, kraken2lib.pm
GITHUB ghcr.io/autamus/lammps LAMMPS is a classical molecular dynamics code with a focus on materials modeling.
GITHUB ghcr.io/autamus/legion Legion is a data-centric parallel programming system for writing portable high performance programs targeted at distributed heterogeneous architectures. legion_prof.py, legion_serializer.py, legion_spy.py
GITHUB ghcr.io/autamus/libnrm Libnrm, the application instrumentation library for the Node Resource Manager(NRM).
GITHUB ghcr.io/autamus/libpng libpng is the official PNG reference library. libpng-config, libpng16-config, png-fix-itxt, pngfix
GITHUB ghcr.io/autamus/libquo QUO (as in status quo) is a runtime library that aids in accommodating thread-level heterogeneity in dynamic, phased MPI+X applications comprising single- and multi-threaded libraries. quo-info
GITHUB ghcr.io/autamus/libtiff Libtiff is a library for reading and writing Tagged Image File Format (abbreviated TIFF) files. fax2tiff, ppm2tiff, raw2tiff, tiff2bw, tiff2pdf, tiff2ps, tiff2rgba, tiffcmp, tiffcp, tiffcrop, tiffdither, tiffdump, tiffinfo, tiffmedian, tiffset, tiffsplit
GITHUB ghcr.io/autamus/libunwind A portable and efficient C programming interface (API) to determine the call-chain of a program.
GITHUB ghcr.io/autamus/libxpm The X PixMap image format is an extension of the monochrome X BitMap format specified in the X protocol, and is commonly used in traditional X applications.
GITHUB ghcr.io/autamus/lmod The Persistence of Vision Ray Tracer, most commonly acronymed as POV-Ray, is a cross-platform ray-tracing program that generates images from a text-based scene description. module
GITHUB ghcr.io/autamus/loki Loki is a C++ library of designs, containing flexible implementations of common design patterns and idioms.
GITHUB ghcr.io/autamus/lp-solve Lp_solve is freely available (under LGPL 2) software for solving linear, integer and mixed integer programs. lp_solve
GITHUB ghcr.io/autamus/mafft MAFFT is a multiple sequence alignment program for unix-like operating systems. mafft, mafft-distance, mafft-einsi, mafft-fftns, mafft-fftnsi, mafft-ginsi, mafft-linsi, mafft-nwns, mafft-nwnsi, mafft-profile, mafft-qinsi, mafft-xinsi
GITHUB ghcr.io/autamus/meme The MEME suite provides online tools for discovering and using protein and DNA sequence motifs. meme, meme-chip, memhog
GITHUB ghcr.io/autamus/mercurial Mercurial is a distributed revision control tool for software developers. hg
GITHUB ghcr.io/autamus/mercury Mercury is a C library for implementing RPC, optimized for HPC
GITHUB ghcr.io/autamus/metall A Persistent Memory Allocator For Data-Centric Analytics
GITHUB ghcr.io/autamus/migrate Migrate estimates effective population sizes and past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes migrate-n
GITHUB ghcr.io/autamus/mothur A single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. mothur
GITHUB ghcr.io/autamus/mpc mithi/mpc: A software pipeline using the Model Predictive Control method to drive a car around a virtual track.
GITHUB ghcr.io/autamus/mpfr The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
GITHUB ghcr.io/autamus/mummer MUMmer is a system for rapidly aligning entire genomes. mummer, mummerplot
GITHUB ghcr.io/autamus/muscle Multiple Sequence Alignment. muscle
GITHUB ghcr.io/autamus/nco nc-config, ncap2, ncatted, ncbo, ncclimo, nccopy, ncdiff, ncdump, ncea, ncecat, nces, ncflint, ncgen, ncgen3, ncks, ncpdq, ncra, ncrcat, ncremap, ncrename, ncurses6-config, ncursesw6-config, ncwa
GITHUB ghcr.io/autamus/ninja Ninja is a small build system with a focus on speed. ninja, ninja-build
GITHUB ghcr.io/autamus/node-js A JavaScript runtime built on Chrome's V8 JavaScript engine. node
GITHUB ghcr.io/autamus/octave GNU Octave is a high-level interpreted language, primarily intended for numerical computations (like an open source Matlab) octave, octave-6.2.0, octave-cli, octave-cli-6.2.0, octave-config, octave-config-6.2.0
GITHUB ghcr.io/autamus/omega-h Omega_h is a C++11 library providing data structures and algorithms for adaptive discretizations.
GITHUB ghcr.io/autamus/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. obabel, obconformer, obdistgen, obenergy, obfit, obfitall, obgen, obgrep, obminimize, obmm, obprobe, obprop, obrms, obrotamer, obrotate, obspectrophore, obsym, obtautomer, obthermo
GITHUB ghcr.io/autamus/opencv OpenCV is a library of programming functions mainly aimed at real-time computer vision. Originally developed by Intel, it was later supported by Willow Garage then Itseez. opencv_version, setup_vars_opencv4.sh
GITHUB ghcr.io/autamus/openjdk Open Java Development Kit jaotc, jar, jarsigner, java, javac, javadoc, javap, jcmd, jconsole, jdb, jdeps, jfr, jhsdb, jimage, jinfo, jjs, jlink, jmap, jmod, jps, jrunscript, jshell, jstack, jstat, jstatd
GITHUB ghcr.io/autamus/openmpi An open source Message Passing Interface implementation. mpiCC, mpic++, mpicc, mpicxx, mpiexec, mpif77, mpif90, mpifort, mpirun, ompi-clean, ompi-server, ompi_info
GITHUB ghcr.io/autamus/pandaseq A program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. pandaseq, pandaseq-checkid, pandaseq-diff, pandaseq-hang, pandaxs
GITHUB ghcr.io/autamus/papi Performance Application Programming Interface. papi_avail, papi_clockres, papi_command_line, papi_component_avail, papi_cost, papi_decode, papi_error_codes, papi_event_chooser, papi_hl_output_writer.py, papi_mem_info, papi_multiplex_cost, papi_native_avail, papi_version, papi_xml_event_info
GITHUB ghcr.io/autamus/papyrus Parallel Aggregate Persistent Storage
GITHUB ghcr.io/autamus/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. pnetcdf-config, pnetcdf_version
GITHUB ghcr.io/autamus/pdt Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools.
GITHUB ghcr.io/autamus/perl The Perl programming language. perl, perlbug, perldoc, perlivp, perlthanks
GITHUB ghcr.io/autamus/petsc PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.
GITHUB ghcr.io/autamus/phist The Pipelined, Hybrid-parallel Iterative Solver Toolkit provides implementations of and interfaces to block iterative solvers for sparse linear and eigenvalue problems. phist_Danasazi_krylov_schur, phist_Danasazi_lobpcg, phist_Dbelos_bgmres, phist_Dbelos_bpcg, phist_Dblockedbicgstab, phist_Dblockedgmres, phist_Dblockedpcg, phist_Dsimple_lanczos, phist_Dsubspacejada, phist_carp_cg
GITHUB ghcr.io/autamus/picard A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. picard, picard.jar
GITHUB ghcr.io/autamus/plasma Parallel Linear Algebra Software for Multicore Architectures, PLASMA is a software package for solving problems in dense linear algebra using multicore processors and Xeon Phi coprocessors. plasmatest
GITHUB ghcr.io/autamus/plink PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. plink
GITHUB ghcr.io/autamus/poppler Poppler is a free software utility library for rendering Portable Document Format (PDF) documents. pdfattach, pdfdetach, pdffonts, pdfimages, pdfinfo, pdfseparate, pdftohtml, pdftops, pdftotext, pdfunite, png-fix-itxt, pngfix
GITHUB ghcr.io/autamus/povray The Persistence of Vision Ray Tracer, most commonly acronymed as POV-Ray, is a cross-platform ray-tracing program that generates images from a text-based scene description. povray
GITHUB ghcr.io/autamus/precice preCICE (Precise Code Interaction Coupling Environment) is a coupling library for partitioned multi-physics simulations.
GITHUB ghcr.io/autamus/prodigal Prodigal Gene Prediction Software prodigal
GITHUB ghcr.io/autamus/proj PROJ is a generic coordinate transformation software, that transforms coordinates from one coordinate reference system (CRS) to another. proj, projinfo, projsync
GITHUB ghcr.io/autamus/protobuf Protocol Buffers is a method of serializing structured data. It is useful in developing programs to communicate with each other over a network or for storing data. protoc, protoc-3.15.8.0
GITHUB ghcr.io/autamus/pumi SCOREC RPI's Parallel Unstructured Mesh Infrastructure (PUMI). print_pumipic_partition
GITHUB ghcr.io/autamus/py-libensemble Library for managing ensemble-like collections of computations.
GITHUB ghcr.io/autamus/py-petsc4py This package provides Python bindings for the PETSc package.
GITHUB ghcr.io/autamus/python An interpreted, high-level and general-purpose programming language. pydoc3, pydoc3.8, python, python-config, python3, python3-config, python3.8, python3.8-config, python3.8-gdb.py
GITHUB ghcr.io/autamus/qhull Snappy (previously known as Zippy) is a fast data compression and decompression library written in C++ by Google based on ideas from LZ77 and open-sourced in 2011. qconvex, qdelaunay, qhalf, qhull, qvoronoi, rbox
GITHUB ghcr.io/autamus/r-seqlogo Sequence logos for DNA sequence alignments
GITHUB ghcr.io/autamus/r R is a language and environment for statistical computing and graphics. R
GITHUB ghcr.io/autamus/raxml RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analysis of large datasets under maximum likelihood. raxmlHPC, raxmlHPC-AVX, raxmlHPC-MPI, raxmlHPC-MPI-AVX, raxmlHPC-MPI-SSE3, raxmlHPC-SSE3
GITHUB ghcr.io/autamus/rclone Rclone is a command line program to manage files on cloud storage. rclone
GITHUB ghcr.io/autamus/rempi ReMPI is a record-and-replay tool for MPI applications. rempi, rempi_record, rempi_replay, reset
GITHUB ghcr.io/autamus/rsync An open source utility that provides fast incremental file transfer. https://rsync.samba.org/ rsync, rsync-ssl
GITHUB ghcr.io/autamus/ruby An interpreted, high-level, general-purpose programming language. bundle, bundler, erb, gem, irb, racc, rake, rbs, rdoc, ri, ruby
GITHUB ghcr.io/autamus/rust Rust is a multi-paradigm programming language designed for performance and safety, especially safe concurrency. cargo, cargo-clippy, cargo-fmt, clippy-driver, rust, rust-gdb, rust-gdbgui, rust-lldb, rustc, rustdoc, rustfmt
GITHUB ghcr.io/autamus/salmon Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. salmon
GITHUB ghcr.io/autamus/samtools Samtools is a suite of programs for interacting with high-throughput sequencing data. blast2sam.pl, bowtie2sam.pl, export2sam.pl, fasta-sanitize.pl, interpolate_sam.pl, novo2sam.pl, psl2sam.pl, sam2vcf.pl, samtools, samtools.pl, seq_cache_populate.pl, soap2sam.pl, wgsim_eval.pl, zoom2sam.pl
GITHUB ghcr.io/autamus/scons SCons is an Open Source software construction tool. scons, scons-3.1.2, scons-3.1.2.bat, scons-configure-cache, scons-configure-cache-3.1.2, scons-time, scons-time-3.1.2, scons.bat, sconsign, sconsign-3.1.2
GITHUB ghcr.io/autamus/scr SCR caches checkpoint data in storage on the compute nodes of a Linux cluster to provide a fast, scalable checkpoint/restart capability for MPI codes. scancel, scontrol, scp, scr_check_node, scr_ckpt_interval.py, scr_copy, scr_crc32, scr_env, scr_flush_file, scr_get_jobstep_id, scr_glob_hosts, scr_halt, scr_halt_cntl, scr_index, scr_inspect, scr_kill_jobstep, scr_list_dir, scr_list_down_nodes, scr_log_event, scr_log_transfer, scr_nodes_file, scr_postrun, scr_prefix, scr_prerun, scr_print, scr_rebuild_partner, scr_rebuild_rs, scr_rebuild_xor, scr_retries_halt, scr_run, scr_scavenge, scr_srun, scr_test_datemanip, scr_test_runtime, scr_watchdog, scrlog.py, scrontab
GITHUB ghcr.io/autamus/siesta SIESTA performs electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. siesta
GITHUB ghcr.io/autamus/slate The Software for Linear Algebra Targeting Exascale (SLATE) project is to provide fundamental dense linear algebra capabilities to the US Department of Energy and to the high-performance computing (HPC) community at large.
GITHUB ghcr.io/autamus/slepc Scalable Library for Eigenvalue Problem Computations.
GITHUB ghcr.io/autamus/snappy Snappy (previously known as Zippy) is a fast data compression and decompression library written in C++ by Google based on ideas from LZ77 and open-sourced in 2011.
GITHUB ghcr.io/autamus/spades St. Petersburg genome assembler – an assembly toolkit containing various assembly pipelines. spades-bwa, spades-convert-bin-to-fasta, spades-core, spades-corrector-core, spades-gbuilder, spades-gmapper, spades-gsimplifier, spades-hammer, spades-ionhammer, spades-kmer-estimating, spades-kmercount, spades-read-filter, spades-truseq-scfcorrection, spades.py, spaligner
GITHUB ghcr.io/autamus/sparsehash several hash-map implementations, similar in API to SGI's hash_map class, but with different performance characteristics.
GITHUB ghcr.io/autamus/sqlite SQLite is a relational database management system contained in a C library. sqlite3
GITHUB ghcr.io/autamus/stc The Swift-Turbine Compiler (STC) stc, swift-t
GITHUB ghcr.io/autamus/stringtie StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. stringtie
GITHUB ghcr.io/autamus/superlu SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.
GITHUB ghcr.io/autamus/sz Error-bounded Lossy Compressor for HPC Data sz
GITHUB ghcr.io/autamus/tasmanian The Toolkit for Adaptive Stochastic Modeling and Non-Intrusive ApproximatioN is a robust library for high dimensional integration and interpolation as well as parameter calibration. https://tasmanian.ornl.gov tasgrid
GITHUB ghcr.io/autamus/tau A portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, UPC, Java, Python.
GITHUB ghcr.io/autamus/tcsh tcsh
GITHUB ghcr.io/autamus/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.
GITHUB ghcr.io/autamus/turbine Turbine is the Swift/T runtime turbine, turbine-pilot, turbine-read-doubles, turbine-write-doubles
GITHUB ghcr.io/autamus/udunits The UDUNITS package supports units of physical quantities. Its C library provides for arithmetic manipulation of units and for conversion of numeric values between compatible units. udunits2
GITHUB ghcr.io/autamus/umap Umap is a library that provides an mmap()-like interface to a simple, user-space page fault handler based on the userfaultfd Linux feature (starting with 4.3 linux kernel).
GITHUB ghcr.io/autamus/unifyfs User level file system that enables applications to use node-local storage as burst buffers for shared files. unifyfs, unifyfs-config, unifyfsd
GITHUB ghcr.io/autamus/unixodbc unixODBC-Test containing Qt based ODBC test tool, and autotest framework. odbc_config, odbcinst
GITHUB ghcr.io/autamus/upcxx UPC++ is a C++ library that supports Partitioned Global Address Space (PGAS) programming, and is designed to interoperate smoothly and efficiently with MPI, OpenMP, CUDA and AMTs. upcxx, upcxx-meta, upcxx-run, upcxx.sh
GITHUB ghcr.io/autamus/valgrind A suite of tools for debugging and profiling. valgrind, valgrind-di-server, valgrind-listener
GITHUB ghcr.io/autamus/veloc Very-Low Overhead Checkpointing System. VELOC is a multi-level checkpoint-restart runtime for HPC supercomputing infrastructures veloc-backend, veloc_check_node, veloc_env, veloc_glob_hosts, veloc_jsrun, veloc_list_down_nodes
GITHUB ghcr.io/autamus/wget GNU Wget is a free software package for retrieving files using HTTP, HTTPS, FTP and FTPS, the most widely used Internet protocols. wget
GITHUB ghcr.io/autamus/xnnpack High-efficiency floating-point neural network inference operators for mobile, server, and Web
GITHUB ghcr.io/autamus/xrootd XRootD software framework is a fully generic suite for fast, low latency and scalable data access, which can serve natively any kind of data, organized as a hierarchical filesystem-like namespace, based on the concept of directory. xrdacctest, xrdadler32, xrdcopy, xrdcp, xrdfs, xrdgsiproxy, xrdgsitest, xrdmapc, xrdpfc_print, xrdpinls, xrdpwdadmin, xrdsssadmin, xrootd, xrootd-config
GITHUB ghcr.io/autamus/xz XZ Utils is free general-purpose data compression software with a high compression ratio. xz, xzcat, xzcmp, xzdec, xzdiff, xzegrep, xzfgrep, xzgrep, xzless, xzmore
GITHUB ghcr.io/autamus/zfp zfp is a compressed number format for multidimensional floating-point and integer arrays.
GITHUB ghcr.io/autamus/zlib zlib is a software library used for data compression. zlib was written by Jean-loup Gailly and Mark Adler and is an abstraction of the DEFLATE compression algorithm used in their gzip file compression program.
GITHUB golang Go (a.k.a., Golang) is a programming language first developed at Google. go, gofmt
GITHUB gradle Gradle is a build tool with a focus on build automation and support for multi-language development. gradle
GITHUB jupyter/datascience-notebook Jupyter Datascience Notebook from https://github.com/jupyter/docker-stacks run-notebook
GITHUB jupyter/minimal-notebook Jupyter Minimal Notebook from https://github.com/jupyter/docker-stacks run-notebook
GITHUB jupyter/pyspark-notebook Jupyter Pyspark Notebook from https://github.com/jupyter/docker-stacks run-notebook
GITHUB jupyter/r-notebook Jupyter R Notebook from https://github.com/jupyter/docker-stacks run-notebook
GITHUB jupyter/scipy-notebook Jupyter Notebook Scientific Python Stack from https://github.com/jupyter/docker-stacks run-notebook
GITHUB jupyter/tensorflow-notebook Jupyter Tensorflow Notebook from https://github.com/jupyter/docker-stacks run-notebook
GITHUB kibana Kibana gives shape to any kind of data — structured and unstructured — indexed in Elasticsearch. kibana, kibana-encryption-keys, kibana-keystore, kibana-plugin
GITHUB mariadb MariaDB Server is one of the most popular database servers in the world. It’s made by the original developers of MySQL and guaranteed to stay open source. Notable users include Wikipedia, DBS Bank and ServiceNow. mariabackup, mariadb, mariadb-access, mariadb-admin, mariadb-analyze, mariadb-backup, mariadb-binlog, mariadb-check, mariadb-conv, mariadb-convert-table-format, mariadb-dump, mariadb-dumpslow, mariadb-find-rows, mariadb-fix-extensions, mariadb-hotcopy, mariadb-import, mariadb-install-db, mariadb-optimize, mariadb-plugin, mariadb-repair, mariadb-report, mariadb-secure-installation, mariadb-service-convert, mariadb-setpermission, mariadb-show, mariadb-slap, mariadb-tzinfo-to-sql, mariadb-upgrade, mariadb-waitpid, mariadbcheck, mariadbd-multi, mariadbd-safe, mariadbd-safe-helper
GITHUB mongo MongoDB is a free and open-source cross-platform document-oriented database program. Classified as a NoSQL database program, MongoDB uses JSON-like documents with schemata. mongo, mongod, mongodump, mongoexport, mongofiles, mongoimport, mongos, mongostat, mongostore, mongotop
GITHUB mysql MySQL is the world's most popular open source database. mysql, mysql_config_editor, mysql_secure_installation, mysql_ssl_rsa_setup, mysql_tzinfo_to_sql, mysql_upgrade, mysqladmin, mysqlbinlog, mysqlcheck, mysqld_multi, mysqld_safe, mysqldump, mysqldumpslow, mysqlimport, mysqlpump, mysqlshow, mysqlslap
GITHUB ncbi/blast The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.
GITHUB nginx Nginx (pronounced 'engine-x') is an open source reverse proxy server for HTTP, HTTPS, SMTP, POP3, and IMAP protocols, as well as a load balancer, HTTP cache, and a web server (origin server). nginx, nginx-debug
GITHUB node Node.js is a software platform for scalable server-side and networking applications. node, nodejs, npm, npx, yarn, yarnpkg
GITHUB nvcr.io/hpc/autodock The AutoDock-GPU Suite is a growing collection of methods for computational docking and virtual screening, for use in structure-based drug discovery and exploration of the basic mechanisms of biomolecular structure and function. More info on AutoDock-GPU be located at https://ccsb.scripps.edu/autodock/ and https://github.com/ccsb-scripps/AutoDock-GPU#usage. autodock
GITHUB nvcr.io/hpc/gromacs GROMACS is a popular molecular dynamics application used to simulate proteins and lipids. python
GITHUB nvcr.io/hpc/lammps Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a software application designed for molecular dynamics simulations. It has the potentials for solid-state materials (metals, semiconductor), soft matter (biomolecules, polymers), and coarse-grained or mesoscopic systems. The main use-case is atom scale particle modeling or, more generically, as a parallel particle simulator at the atomic, meson, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. Read more on the LAMMPS website https://lammps.sandia.gov/.
GITHUB nvcr.io/hpc/namd NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-comp atible with AMBER, CHARMM, and X-PLOR. charmrun, flipbinpdb, flipdcd, namd3, psfgen, sortreplicas, vmd
GITHUB nvcr.io/hpc/preflightcheck The Pre-Flight Check container verifies that the container runtime is setup correctly for GPUs and InfiniBand.
GITHUB nvcr.io/hpc/quantum_espresso Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale based on density-functional theory, plane waves, and pseudopotentials.
GITHUB nvcr.io/nvidia/caffe NVIDIA Caffe, also known as NVCaffe, is an NVIDIA-maintained fork of Berkeley Vision and Learning Center (BVLC) Caffe tuned for NVIDIA GPUs, particularly in multi-GPU configurations. python
GITHUB nvcr.io/nvidia/digits The NVIDIA Deep Learning GPU Training System (DIGITS) puts the power of deep learning into the hands of engineers and data scientists. python
GITHUB nvcr.io/nvidia/hpc-benchmarks The NVIDIA HPC-Benchmarks collection provides three NVIDIA accelerated HPC benchmarks: HPL-NVIDIA, HPL-AI-NVIDIA, and HPCG-NVIDIA.
GITHUB nvcr.io/nvidia-hpcvis/paraview ParaView is one of the most popular visualization software for analyzing HPC datasets. pvdataserver, pvrenderserver, pvbatch, pypython, pvserver
GITHUB nvcr.io/nvidia/pytorch PyTorch is a GPU accelerated tensor computational framework with a Python front end. Functionality can be easily extended with common Python libraries such as NumPy, SciPy, and Cython. Automatic differentiation is done with a tape-based system at both a functional and neural network layer level.
GITHUB nvcr.io/nvidia/rapidsai/rapidsai The RAPIDS suite of software libraries gives you the freedom to execute end-to-end data science and analytics pipelines entirely on GPUs. python
GITHUB nvcr.io/nvidia/tensorflow TensorFlow is an open-source software library for high-performance numerical computation. Its flexible architecture allows easy deployment of computation across a variety of platforms (CPUs, GPUs, TPUs), and from desktops to clusters of servers to mobile and edge devices.
GITHUB openjdk OpenJDK is an open-source implementation of the Java Platform, Standard Edition. jar, jarsigner, java, javac, javadoc, javap, jcmd, jconsole, jdb, jdeprscan, jdeps, jfr, jhsdb, jimage, jinfo, jlink, jmap, jmod, jobs, join, jpackage, jps, jrunscript, jshell, jstack, jstat, jstatd
GITHUB php While designed for web development, the PHP scripting language also provides general-purpose use. php, php-cgi, php-config, phpdbg, phpize
GITHUB poldracklab/mriqc Automatic prediction of quality and visual reporting of MRI scans. mriqc
GITHUB postgres PostgreSQL, often simply 'Postgres', is an object-relational database management system (ORDBMS) with an emphasis on extensibility and standards-compliance. clusterdb, createdb, createuser, dropdb, dropuser, initdb, oid2name, pg_archivecleanup, pg_basebackup, pg_checksums, pg_config, pg_controldata, pg_ctl, pg_dump, pg_dumpall, pg_isready, pg_receivewal, pg_recvlogical, pg_resetwal, pg_restore, pg_rewind, pg_standby, pg_test_fsync, pg_test_timing, pg_upgrade, pg_verifybackup, pg_waldump, pgbench, postgres, postmaster, psql, reindexdb, vacuumdb, vacuumlo
GITHUB python An interpreted, high-level and general-purpose programming language. python
GITHUB quay.io/biocontainers/bamtools C++ API and command-line toolkit for working with BAM data. bamtools
GITHUB quay.io/biocontainers/bbmap BBMap is a short read aligner, as well as various other bioinformatic tools. a_sample_mt.sh, addadapters.sh, addssu.sh, adjusthomopolymers.sh, alltoall.sh, analyzeaccession.sh, analyzegenes.sh, analyzesketchresults.sh, applyvariants.sh, bbcms.sh, bbcountunique.sh, bbduk.sh, bbest.sh, bbfakereads.sh, bbmap.sh, bbmapskimmer.sh, bbmask.sh, bbmerge-auto.sh, bbmerge.sh, bbnorm.sh, bbrealign.sh, bbrename.sh, bbsketch.sh, bbsplit.sh, bbsplitpairs.sh, bbstats.sh, bbversion.sh, bbwrap.sh, bloomfilter.sh, build_env_setup.sh, calcmem.sh, calctruequality.sh, callgenes.sh, callpeaks.sh, callvariants.sh, callvariants2.sh, clumpify.sh, commonkmers.sh, comparegff.sh, comparesketch.sh, comparessu.sh, comparevcf.sh, conda_build.sh, consect.sh, consensus.sh, countbarcodes.sh, countgc.sh, countsharedlines.sh, crossblock.sh, crosscontaminate.sh, cutgff.sh, cutprimers.sh, decontaminate.sh, dedupe.sh, dedupe2.sh, dedupebymapping.sh, demuxbyname.sh, diskbench.sh, estherfilter.sh, explodetree.sh, fetchproks.sh, filterassemblysummary.sh, filterbarcodes.sh, filterbycoverage.sh, filterbyname.sh, filterbysequence.sh, filterbytaxa.sh, filterbytile.sh, filterlines.sh, filterqc.sh, filtersam.sh, filtersilva.sh, filtersubs.sh, filtervcf.sh, fixgaps.sh, fungalrelease.sh, fuse.sh, gbff2gff.sh, getreads.sh, gi2ancestors.sh, gi2taxid.sh, gitable.sh, grademerge.sh, gradesam.sh, icecreamfinder.sh, icecreamgrader.sh, icecreammaker.sh, idmatrix.sh, idtree.sh, invertkey.sh, kapastats.sh, kcompress.sh, keepbestcopy.sh, khist.sh, kmercountexact.sh, kmercountmulti.sh, kmercoverage.sh, kmerfilterset.sh, kmerlimit.sh, kmerlimit2.sh, kmerposition.sh, kmutate.sh, lilypad.sh, loadreads.sh, loglog.sh, makechimeras.sh, makecontaminatedgenomes.sh, makepolymers.sh, mapPacBio.sh, matrixtocolumns.sh, mergeOTUs.sh, mergebarcodes.sh, mergepgm.sh, mergeribo.sh, mergesam.sh, mergesketch.sh, mergesorted.sh, msa.sh, mutate.sh, muxbyname.sh, partition.sh, phylip2fasta.sh, pileup.sh, plotflowcell.sh, plotgc.sh, postfilter.sh, printtime.sh, processfrag.sh, processhi-c.sh, processspeed.sh, randomgenome.sh, randomreads.sh, readlength.sh, readqc.sh, reducesilva.sh, reformat.sh, reformatpb.sh, removebadbarcodes.sh, removecatdogmousehuman.sh, removehuman.sh, removehuman2.sh, removemicrobes.sh, removesmartbell.sh, rename.sh, renameimg.sh, repair.sh, replaceheaders.sh, representative.sh, rqcfilter.sh, rqcfilter2.sh, runhmm.sh, samtoroc.sh, seal.sh, sendsketch.sh, shred.sh, shrinkaccession.sh, shuffle.sh, shuffle2.sh, sketch.sh, sketchblacklist.sh, sketchblacklist2.sh, sortbyname.sh, splitbytaxa.sh, splitnextera.sh, splitribo.sh, splitsam.sh, splitsam4way.sh, splitsam6way.sh, stats.sh, statswrapper.sh, streamsam.sh, subsketch.sh, summarizecontam.sh, summarizecoverage.sh, summarizecrossblock.sh, summarizemerge.sh, summarizequast.sh, summarizescafstats.sh, summarizeseal.sh, summarizesketch.sh, synthmda.sh, tadpipe.sh, tadpole.sh, tadwrapper.sh, taxonomy.sh, taxserver.sh, taxsize.sh, taxtree.sh, testfilesystem.sh, testformat.sh, testformat2.sh, tetramerfreq.sh, textfile.sh, translate6frames.sh, unicode2ascii.sh, unzip.sh, vcf2gff.sh, webcheck.sh
GITHUB quay.io/biocontainers/bcftools BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. bcftools, bgzip, color-chrs.pl, guess-ploidy.py, htsfile, tabix, vcfutils.pl
GITHUB quay.io/biocontainers/beast2 BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. beast, beauti, densitree, treeannotator
GITHUB quay.io/biocontainers/bedtools Bedtools is the swiss army knife for genome arithmetic. bedtools
GITHUB quay.io/biocontainers/blast BLAST finds regions of similarity between biological sequences. blast_formatter, blastdb_aliastool, blastdbcheck, blastdbcmd, blastn, blastp, blastx, cleanup-blastdb-volumes.py, convert2blastmask, deltablast, eblast, makeblastdb, psiblast, rpsblast, rpstblastn, tblastn, tblastx, update_blastdb.pl
GITHUB quay.io/biocontainers/bowtie2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. bowtie2, bowtie2-align-l, bowtie2-align-s, bowtie2-build, bowtie2-build-l, bowtie2-build-s, bowtie2-inspect, bowtie2-inspect-l, bowtie2-inspect-s
GITHUB quay.io/biocontainers/bracken A highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. bracken, bracken-build, combine_bracken_outputs.py, est_abundance.py, generate_kmer_distribution.py, kmer2read_distr
GITHUB quay.io/biocontainers/bwa-mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in BWA. bwa-mem2
GITHUB quay.io/biocontainers/bwa BWA is a program for aligning sequencing reads against a large reference genome. bwa
GITHUB quay.io/biocontainers/canu Canu is a fork of the celera assembler designed for high-noise single-molecule sequencing canu
GITHUB quay.io/biocontainers/clustalo Multiple sequence alignment program for aligning 3+ sequences together clustalo
GITHUB quay.io/biocontainers/cutadapt Trim adapters from high-throughput sequencing reads cutadapt
GITHUB quay.io/biocontainers/diamond Accelerated blast compatible local sequence aligner diamond
GITHUB quay.io/biocontainers/fastp An ultra-fast all-in-one FASTQ preprocessor. fastp
GITHUB quay.io/biocontainers/fastqc A quality control tool for high throughput sequence data fastqc
GITHUB quay.io/biocontainers/gatk4 An open source toolkit frequently used by most genomic research and clinical analyses gatk
GITHUB quay.io/biocontainers/kraken2 A taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. kraken2, kraken2-build, kraken2-inspect
GITHUB quay.io/biocontainers/maker A portable and easily configurable genome annotation pipeline maker
GITHUB quay.io/biocontainers/mrbayes A program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models mb
GITHUB quay.io/biocontainers/multiqc Aggregate results from bioinformatics analyses across many samples into a single report. multiqc
GITHUB quay.io/biocontainers/mummer MUMmer is a system for rapidly aligning entire genomes in complete or in draft form. mummer
GITHUB quay.io/biocontainers/salmon Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. salmon
GITHUB quay.io/biocontainers/sambamba Sambamba is a high performance highly parallel robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. sambamba
GITHUB quay.io/biocontainers/samtools Tools for reading/writing/editing/indexing/viewing SAM/BAM/CRAM format. bgzip, htsfile, samtools, tabix
GITHUB quay.io/biocontainers/spades SPAdes – St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines. spades.py
GITHUB quay.io/biocontainers/star Spliced Transcripts Alignment to a Reference. STAR
GITHUB quay.io/biocontainers/trimmomatic A flexible read trimming tool for Illumina NGS data. trimmomatic
GITHUB quay.io/biocontainers/trinity Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity, trinity
GITHUB quay.io/biocontainers/vcftools A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project. vcftools
GITHUB quay.io/biocontainers/velvet Short read de novo assembler using de Bruijn graphs velvetg, velveth
GITHUB quay.io/vgteam/vg Tools for working with genomic variation graphs. https://github.com/vgteam/vg vg
GITHUB r-base R is a system for statistical computation and graphics. R, Rscript
GITHUB rabbitmq RabbitMQ is an open source multi-protocol messaging broker. rabbitmq-defaults, rabbitmq-diagnostics, rabbitmq-env, rabbitmq-plugins, rabbitmq-queues, rabbitmq-server, rabbitmq-upgrade, rabbitmqctl
GITHUB redis Redis is an open-source, networked, in-memory, key-value data store with optional durability. redis-benchmark, redis-check-aof, redis-check-rdb, redis-cli, redis-sentinel, redis-server
GITHUB rocker/ml-verse Machine learning in R. R, Rscript, rocker-ml-run, rocker-ml-verse-run, rserver, rserver-pam, rsession, rstudio-server
GITHUB rocker/ml Docker images with R + machine learning libraries (CPU versions). R, Rscript, rocker-ml-run, rserver, rserver-pam, rsession, rstudio-server
GITHUB rocker/rstudio Rstudio server image R, Rscript, rocker-rstudio-run, rserver, rserver-pam, rsession, rstudio-server
GITHUB rocker/shiny Docker image with R + Shiny. rocker-shiny-run, shiny-server
GITHUB rocker/tidyverse Version-stable build of R, rstudio, and R packages R, Rscript, rocker-ml-run, rocker-tidyverse-run, rserver, rserver-pam, rsession, rstudio-server
GITHUB ruby Ruby is a dynamic, reflective, object-oriented, general-purpose, open-source programming language. bundle, bundler, erb, gem, irb, racc, rake, rbs, rdoc, ri, ruby, typeprof
GITHUB singularityhub/singularity-deploy Example shpc container using Singularity Deploy, build and serve from GitHub releases. salad
GITHUB solr Solr is the popular, blazing-fast, open source enterprise search platform built on Apache Lucene™. post, postlogs, solr
GITHUB spack/ubuntu-bionic Ubuntu 18.04 with Spack preinstalled. sbang, spack, spack-python
GITHUB tensorflow/tensorflow An end-to-end open source platform for machine learning. python
GITHUB tomcat Apache Tomcat is an open source implementation of the Java Servlet and JavaServer Pages technologies
GITHUB uvarc/qiime2 QIIME2. Same functionality as the official image but less than half the size. Includes packages Empress and PICRUSt2.
GITHUB vanessa/salad A container all about fork and spoon puns. salad
GITHUB vault Vault is a tool for securely accessing secrets via a unified interface and tight access control. vault