Galaxy Platform Directory: Servers, Clouds, and Deployable Resources
This directory lists platforms where you can use or deploy your own Galaxy Server with minimal effort.
- Almost all of them are free to use (Commercial clouds are the exception)
- Almost all of them are open to everyone (Academic clouds are the exception).
- All of the resources can be used, either immediately, or shortly after getting an account.
These resources cover a wide spectrum of domains all across life sciences. There are resources for genomics (lots of them), metagenomics, transcriptomics, proteomics, drug discovery and even some outside biology like natural language processing (a couple of them), and social science.
UseGalaxy Resources
UseGalaxy servers implement a common core set of tools and reference genomes, and are open to anyone to use. They also contain tools and genomes that are local to each server. Each is backed by significant computational resources and they are excellent places to get started with Galaxy, and to share and publish your results.
| Resource | Server | Summary | Keywords |
|---|---|---|---|
| UseGalaxy.eu | Server | The European UseGalaxy server. | UseGalaxy |
| UseGalaxy.org (Main) | Server | The Galaxy Project free public server; biomedical research | UseGalaxy |
| UseGalaxy.org.au | Server | The Australian UseGalaxy server. | UseGalaxy |
All Resources
Complete listing of resources for using Galaxy.
| Resource | Server | Cloud | Deploy- able | Summary | Keywords |
|---|---|---|---|---|---|
| AB-OpenLab | Server | FROG stands for FingeRprinting Ontology of Genomic variations. FROG fingerprints have been devised to capture genomic variations at various levels. | Tools | ||
| ABiMS | Server | Analysis and bioinformatics for Marine Science. | Genomics | ||
| AGEseq @ AspenDB | Server | This site provides a user-friendly interface for AGEseq (Analysis of Genome Editing by Sequencing) in a Galaxy instance. | Tools | ||
| Amazon Web Services (AWS) | Commercial | Set up you own general purpose genomics server runing AWS using GVL and CloudMan. | Genomics | ||
| ANASTASIA | Server | Automated Nucleotide Aminoacid Sequences Translational plAtform for Systemic Interpretation and Analysis | Genomics | ||
| AnVIL | Academic Commercial | Run Galaxy inside the secure AnVIL environment on Google Cloud Platform. | Genomics | ||
| APOSTL | Server | Automated Processing of SAINT Templated Layouts (APOSTL) is a freely available software suite and analysis pipeline for reproducible, interactive analysis of AP-MS data. | Tools | ||
| ARGA | Server | Antibiotic Resistance Gene Analyzer | Domain | ||
| ARGs-OAP | Server | Fast annotation and classification of antibiotic resistance gene-like sequences from metagenomic data. | Domain | ||
| ARIAweb | Server | Automated NOE assignment and NMR structure calculation | Domain | ||
| ARIES | Server | Analysis of genomic data in the field of public health and food safety, with the aim of deploying a comprehensive bioinformatics approach to the study of food-borne zoonoses and infectious diseases at the human and animal interface. | Domain | ||
| ASaiM | Container | Integrates tools specifically chosen for metagenomic and metatranscriptomic studies and hierarchically organized to orient user choice toward the best tool for a given task. | Tools | ||
| ATACgraph | Container | ATAC-seq for biologists with minimal bioinformatics knowledge to analyze chromatin accessibility | Domain | ||
| BF2I-MAP | Server | Locally developed as well as standard tools are available on a 16-core server with 32GB memory, accessible to all users, and located in the BF2I lab. | Tools | ||
| BioBix | Server | A general genomics server. Includes the PROTEOFORMER pipeline tools. | Genomics | ||
| BioCiphers Lab Galaxy | Server | BCL Galaxy gives a user friendly interface for analysis tools developed by the BioCiphers Lab at the University of Pennsylvania. | Tools | ||
| BioCompute Object Galaxy | Server | BioCompute Objects is a standard for communication of High-throughput Sequencing (HTS) analysis results, data set creation and curation, and bioinformatics verification protocols. | Genomics | ||
| BioDivine Toolset | Server | Systems biology tools implemented by the Sybila team. | Tools | ||
| BioMaS | Server | Taxonomic studies of environmental microbial communities | Tools | ||
| Biomina | Server | A general purpose Galaxy instance that includes most standard tools for DNA/RNA sequencing, plus extra tools for panel resequencing, variant annotation and some tools for Illumina SNParray analysis. | Genomics | ||
| BIPAA (BioInformatics Platform for Agroecosystem Arthropods) | Server | Insect genomics (aphids, parasitoïd wasps, lepidopterans) | Domain | ||
| BitLAB | Server | Detailed analysis of metagenomes. | Tools | ||
| BRIDGE | Server | Container | Prepare, simulate and analyse and visualise molecular simulations, especially molecular dynamics and free energies. | Domain | |
| CAFU | Server | Container | A Galaxy framework for exploring unmapped RNA-Seq data | Domain | |
| CBiB Galaxy | Server | A general purpose Galaxy instance that includes EMBOSS (a software analysis package for molecular biology) and fibronectin (diversity analysis of synthetic libraries of a Fibronectin domain). | Genomics | ||
| CellOrganizer for Galaxy | Server | Create generative models of the spatial organization of cells from microscope images and automatically provide geometries for spatial simulations of cell processes and behaviors | Tools | ||
| Center for Phage Technology (CPT) | Server | Phage biology and automated annotation. | Domain | ||
| ChemFlow | Server | Chemometrics without programming: infrared spectrometry on a Galaxy platform. | Domain | ||
| Chemical Annotation Retrieval Toolkit (CART) | Server | Retrieves annotations on biological effects of chemicals and determines which ones are enriched. | Tools | ||
| ChemicalToolbox | Server | Container | For processing, analysing and visualising chemical data, and performing molecular simulations. | Domain | |
| CIRM-CFBP | Server | Web based access to tools (SkIf, KI-S) of IRHS-EmerSys lab. | Tools | ||
| Cistrome Analysis Pipeline | Server | ChIP-chip/seq and gene expression data | Domain | ||
| Climate Science Workbench | Server | A comprehensive set of analysis tools and consolidated workflows for climate analysis and visualisation | Domain | ||
| CLIMB | Academic | The CLIMB project (Cloud Infrastructure for Microbial Bioinformatics) develops and deploys a world leading cyber-infrastructure for microbial bioinformatics; providing free cloud-based compute, storage, and analysis tools for academic microbiologists in the UK. | Genomics | ||
| CLIP-Explorer | Server | The CLIP-Explorer is a webserver to process, analyse and visualise CLIP-Seq data. | Domain | ||
| Codon Harmonizer | Server | Easily generate codon harmonized variants of gene sequences for heterologous expression | Tools | ||
| Coloc-stats | Server | a unified web interface to perform co-localization analysis of genomic features | Domain | ||
| CoralSNP | Server | Standard Tools for Acroporid Genotyping (STAG) | Domain | ||
| CorGAT | Server | Align complete assemblies of SARS-CoV-2 genomes wih the reference genomic sequence, to obtain a list of polymorphic positions and to annotate genetic variants. | Domain | ||
| CoSSci | Server | Tools for solving Galton's problem in Comparative Research and complex network problems in Social Science. | Domain | ||
| COVID-19 | Server | A companion to our study describing the analysis of early COVID-19 data | Domain | ||
| CRAVAT-P | Container | A Docker image containing a fully-operational Galaxy instance with pre-installed demonstration material for CRAVAT-P. | Tools | ||
| deepTS | Server | Container | Explore transcriptional switches from pairwise, temporal, and population RNA-Seq using deepTS. | Tools | |
| Dintor | Server | GWA and NGS tools and modules for functional annotation of genes and gene products | Domain | ||
| DocMethyl EpiMOLAS | Container | Galaxy Docker for DNA methylation analysis in WGBS | Domain | ||
| epiGeEC | Server | Compare user-provided epigenomic datasets with thousands of public datasets. | Tools | ||
| Epigenomics Galaxy | Container | Galaxy Docker image for epigenomics analysis | Domain | ||
| Erasmus MC | Server | General purpose genomics analysis, featuring many standard tools plus many additional tools. | Genomics | ||
| EWAS-Galaxy | Container | Galaxy Docker image for population epigenetics data analysis | Domain | ||
| Excellence in Breeding | Server | Hosts tools for the GOBii project, HTPG project and EiB platform, including genomic selection, marker selection, GWAS, imputation, file conversion, and cluster analysis. | Tools | ||
| FreeBioinfo | Server | Galaxy for metagenomic analysis. | Domain | ||
| G-OnRamp | Commercial | VM | G-OnRamp provides a user-friendly, web-based platform for collaborative, end-to-end annotation of eukaryotic genomes using UCSC Assembly Hubs and JBrowse/Apollo genome browsers with evidence tracks derived from sequence alignments, ab initio gene predictors, RNA-Seq data, and repeat finders. | Domain | |
| GalaxEast | Server | Integrative 'omics data analysis | Genomics | ||
| Galaxy Africa | Server | Devoted to assisting researchers on the African continent accelerate their genomics research and analyses. | Genomics | ||
| Galaxy basic sequence manipulation | Container | Galaxy Docker repository for basic sequence data analysis. | Domain | ||
| Galaxy BLAST+ | Container | A complete and production ready Galaxy instance with installed BLAST+ tools. | Domain | ||
| Galaxy Docker | Container | The Galaxy Docker Image is an easy distributable full-fledged Galaxy installation, that can be used for testing, teaching and presenting new tools and features. | Genomics | ||
| Galaxy Exome-Seq | Container | Galaxy Docker repository for Exome sequencing data analysis | Domain | ||
| Galaxy for Ecology | Server | A web platform to get, process, analyze and visualize ecological data | Domain | ||
| Galaxy Genome Annotation (GGA) | Server | Container | Galaxy for genome annotation | Domain | |
| Galaxy Imaging | Server | Container | Galaxy Docker repository for image analysis | Domain | |
| Galaxy Integrated Omics (GIO) | Server | Proteomics Informed by Transcriptomics (PIT) methodology, and selection of surrogate peptides for targeted proteomics. | Domain | ||
| Galaxy mothur Toolset Docker | Container | Galaxy Docker image for microbial ecology analysis with mothur | Domain | ||
| Galaxy Test | Server | Beta version of Galaxy Main | Genomics | ||
| Galaxy Workbench for Mass Spectrometry Imaging | Container | Galaxy Docker image for mass spec imaging | Domain | ||
| Galaxy-P | Server | Galaxy-P is a multiple 'omics' data analysis platform with particular emphasis on mass spectrometry based proteomics. Galaxy-P is developed at the University of Minnesota, deployed at the Minnesota Supercomputing Institute. | Domain | ||
| Galaxy-SynBioCAD | Server | Synthetic biology and metabolic engineering | Domain | ||
| Galaxy@GenOuest | Server | A general purpose Galaxy server Includes tools developped by Dyliss and GenScale bioinformatics research teams in Rennes, France. | Genomics | ||
| Galaxy@Pasteur | Server | General purpose genomics analysis server. | Genomics | ||
| Galaxy@PRABI | Server | Includes bioinformatics tools developed by the research teams working in the perimeter of the PRABI core facility, including kissplice/kissDE, TETools, SEX-DETector, and priam. | Genomics | ||
| GalaxyTrakr | Server | Supporting food-borne pathogen research | Domain | ||
| GASLINI | Server | Supports PIPE-T, a tool for Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) analysis. | Tools | ||
| GCAC : Galaxy for Compound Activity Classification | Server | VM | GCAC is a web enabled platform for predictive model building using R and caret package for virtual screening. | Tools | |
| GenAP | Academic | All Canadian researchers are eligible for a GenAP account. International researchers that have a Canadian collaborator can also be sponsored and become eligible to a GenAP account as well. | Genomics | ||
| GeneLab | Server | NASA GeneLab is a comprehensive space-related omics database in which users can upload, download, share, store, and analyze spaceflight and corresponding model organism data. | Genomics | ||
| Genomic Hyperbrowser | Server | Statistical methodology and computing power to handle a variety of biological inquires on genomic datasets | Domain | ||
| GigaGalaxy | Server | GigaGalaxy hosts tools and data analyses from papers published in *GigaScience*. | Genomics | ||
| Globus Genomics | Academic Commercial | Globus Genomics provides hardened high-performance Galaxy servers running with Globus on AWS. | Genomics | ||
| GraphClust | Server | Container | GraphClust2 is a workflow for scalable clustering of RNAs based on sequence and secondary structures feature. GraphClust2 is implemented within the Galaxy framework and consists a set of integrated Galaxy tools and flavors of the linear-time clustering workflow. | Tools | |
| GrAPPA | Server | GrAPPA is a web-based interface constructed on the Galaxy framework for graph theoretical tools. It contains novel combinatorial methods integrated into a complete microarray analysis toolchain, from uploading raw high-throughput data to visualization of results. | Domain | ||
| Halogen Bonding | Server | Visualize halogen bond contacts in the protein binding site. Analyze a protein binding site for halogen bonding hotspots. Evaluate halogen contacts with the protein backbone using the scoring function XBScore. | Tools | ||
| Hardwood Genomics | Server | A simplified, workflow-centic interface to Galaxy, focused on genomics data from hardwood trees. | Domain | ||
| HiCExplorer | Server | Tools to process and visualize chromosome conformation. | Domain | ||
| Human Cell Atlas | Server | Tools and workflows for the analysis of Single Cell RNA-Seq data. It includes a module that connects to the Matrix Service API of the Human Cell Atlas’s Data Coordination Platform that enables retrieval of gene expression matrices from any data sets in the Human Cell Atlas. | Domain | ||
| Huttenhower Lab | Server | metagenomic and functional genomic analyses, intended for research and academic use | Domain | ||
| HyPhy HIV NGS Tools | Server | Tools for HIV sequencing analysis. | Domain | ||
| IBERS @ Aberystwyth | Server | Software, tools and pages written by IBERS researchers for release to the wider community. | Tools | ||
| IDENAP | Server | Inter-Domain Ecological Network Analysis Pipeline | Domain | ||
| Image Analysis and Processing Toolkit | Server | Image analysis and processing. | Domain | ||
| ImmPort Galaxy | Server | Flow Cytometry Analysis. | Domain | ||
| immuneML | Server | Machine learning-based analysis and classification of adaptive immune receptors and repertoires (AIRR). | Domain | ||
| InteractoMIX | Server | A one-stop resource offering a wide range of computational analyses from proteome-wide interactomes to structure of protein complexes | Domain | ||
| IPK Galaxy Blast Suite | Server | Part of the IPK Crop Analysis Tools Suite (CATS). Offers access to genomic references published by IPK and collaborative projects | Domain | ||
| Jetstream | Academic | Jetstream is part of XSEDE, a "collection of integrated advanced digital resources and services" and is funded by NSF. | Genomics | ||
| Langille Lab | Server | Prediction of the unobserved character states in a community of organisms from phylogenetic information. | Tools | ||
| Laniakea | Academic | Laniakea provides the possibility to automate the creation of Galaxy-based virtualized environments through an easy setup procedure, providing an on-demand workspace ready to be used by life scientists and bioinformaticians, with built-in storage encryption for user data. | Genomics | ||
| LAPPS Grid | Server | An open, interoperable web service platform for natural language processing (NLP) research and development. | Domain | ||
| Lebanese University Galaxy | Server | Includes the SpCLUST tool set for fast and reliable clustering of potentially divergent biological sequences | Tools | ||
| Lifeportal | Server | a Galaxy instance to satisfy the computational needs of the Norwegian research community in life sciences but also of any other user willing to use the service. | Genomics | ||
| LiSIs | Server | A platform for Virtual Screening. | Tools | ||
| Machine Learning Workbench | Server | A comprehensive set of data preprocessing, machine learning, deep learning and visualisation tools, consolidated workflows for end-to-end machine learning analysis and training materials to showcase the usage of these tools. | Domain | ||
| Majewski Lab | Server | Detection of recurrent Allelic Imbalance in tumors using whole Exome sequencing data. | Tools | ||
| Mandoiu Lab | Server | A customized installation of the Galaxy framework deploying bioinformatic tools and pipelines developed in the Mandoiu Lab at the University of Connecticut for high-throughput sequencing and immunogenomics data analysis | Tools | ||
| MaREA4Galaxy | Server | Metabolic Reaction Enrichment Analysis and visualization of RNA-seq data | Tools | ||
| Martin Luther U. Halle-Wittenberg | Server | Provides implementations of GeMoMa, InMoDe, CRISPRer, TALgetter, TALgetterLong, TALENoffer, and Dimont | Tools | ||
| Metabolomics | Server | A community driven metabolomics Galaxy service | Domain | ||
| MetaCentrum | Academic | MetaCentrum regional virtual organization of the Czech National Grid Infrastructure (NGI) and is accessible to employees and students of research and academic organizations of the Czech Republic and for scientific purposes only. | Genomics | ||
| Metagenomics | Server | a webserver to process, analyse and visualize Metagenomic and Microbiota data in general. | Domain | ||
| Metaproteomics Gateway | Server | Metaproteomics gateway providing access to documentation and other instructional materials, and an opportunity for hands-on training using example datasets and optimized metaproteomics workflows | Domain | ||
| MGS-Fast | Container | Shotgun whole-genome metagenomic analysis using DNA-DNA alignment | Domain | ||
| miCloud | Container | Leverage cloud technologies to provide an easy-to-use streamlined NGS data analysis using local computational hardware | Genomics | ||
| Migale | Server | A general purpose genomics server with an emphasis on metagenomics, including FROGS and several Migale developed tools. | Genomics | ||
| MiModD NacreousMap | Server | NacreousMap mapping/plotting tool of MiModD for users of MiModD who do not want to install the required dependencies (R and rpy2) for graphical output from this tool on their local system. | Tools | ||
| MISSISSIPPI | Server | Support for analyses of RNA and small RNA sequencing datasets as well as for epigenetics or metagenomics studies. | Domain | ||
| Molecular Property Diagnostic Suite - Diabetes Mellitus Portal (MPDSDM) | Server | A disease-specific open source web portal for Diabetes Mellitus. | Domain | ||
| Molecular Property Diagnostic Suite - Tuberculosis (MPDSTB) | Server | A disease-specific web portal for Tuberculosis for drug discovery and development. | Domain | ||
| NanoGalaxy | Server | a webserver to process, analyse and visualize Oxford Nanopore Technologies (ONT) data and similar long-reads technologies. | Domain | ||
| Nectar Cloud | Academic | Set up a Galaxy server on Australia's Nectar research cloud. | Genomics | ||
| NetworkAnalyst | Server | For mapping and quantification of raw RNA-seq data | Domain | ||
| NG-Tax | Server | Container | A Semantic Framework for High-throughput Marker Gene (Amplicon) Analysis | Tools | |
| NGPhylogeny.fr | Server | Container | Robust phylogenetic analysis for everyone. | Domain | |
| Oqtans | Server | Customized Galaxy, extended with machine learning based tools for sequence and tiling array data analysis. | Domain | ||
| Orione | Server | A Galaxy based web server for microbiology. Orione includes all post mapping or assembling steps from scaffolding to complete annotation pipelines. | Domain | ||
| OSDDlinux LiveGalaxy | Server | Drug discovery | Domain | ||
| Osiris | Server | Phylogenetics | Tools | ||
| Palfinder | Server | Microsatellite development. | Tools | ||
| PepSimili | Server | Integrated workflow tool for mapping of massive peptide repertoires on whole proteomes and delivering streamlined, systems-level biological interpretation. | Tools | ||
| PhagePromotor | Server | Predict promoter sequences in phage genomes, using machine learning models. | Tools | ||
| PhenoMeNal | Academic Commercial | Large scale computing for medical informatics | Domain | ||
| PIA | Server | Phylogenetics and gene interaction | Tools | ||
| PiRATE: a Pipeline to Retrieve and Annotate Transposable Elements | VM | Detect, classify and annotate TEs of non-model organisms. | Tools | ||
| Plant Anaylsis Workbench | Server | A community driven plant data analsys Galaxy service | Domain | ||
| PlantGenIE | Server | Plant Genome Integrative Explorer Galaxy instance | Domain | ||
| PreSTIGE | Server | Predicting Specific Tissue Interactions of Genes and Enhancers | Tools | ||
| Proteogenomics Gateway | Server | Provides access to documentation and other instructional materials, and an opportunity for hands-on training using example datasets and optimized proteogenomics workflows. The main goal of this server is to provide documentation to facilitate training and mastery of these software and workflows. | Domain | ||
| ProteoRE | Server | ProteoRE (Proteomics Research Environment) | Domain | ||
| Protologger | Server | All-in-one genome description tool, aimed at simplifying gathering the data required for writing protologues. This includes providing taxonomic, functional and ecological insights. | Tools | ||
| q2Galaxy | Container | QIIME 2 Galaxy Docker image. | Tools | ||
| QuanTP | Container | A Docker image containing a fully-operational Galaxy instance with pre-installed QuanTP tools. | Tools | ||
| RepeatExplorer | Server | Graph-based clustering and characterization of repetitive sequences, and detection of transposable element protein coding domains. | Domain | ||
| RiboGalaxy | Server | Container | Tools for the analysis and visualization of ribo-seq data obtained with the ribosome profiling technique. | Domain | |
| Rice Galaxy | Server | Tools for designing single-nucleotide polymorphism assays, analyzing genome-wide association studies, population diversity, rice−bacterial pathogen diagnostics, and a suite of published genomic prediction methods. | Domain | ||
| RNA Modification Calling | Container | Galaxy Docker image for RNA analysis and modification calling | Tools | ||
| RNA Workbench | Server | Container | more than 50 bioinformatics tools dedicated to different research areas of RNA biology, including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-Seq analysis, and RNA target prediction. | Domain | |
| SARS-CoV-2 ENA Submission | Container | Galaxy Docker image for submitting SARS-CoV-2 data to ENA | Tools | ||
| Sciensano | Server | General purpose Galaxy server optimized for microbiological genomics applications of interest for public health. | Genomics | ||
| Shapiro Lab | VM | RNA structure and design tools including RNA2D3D and StructureLab | Tools | ||
| Single Cell Omics workbench | Server | The Single Cell Omics workbench is a comprehensive set of analysis tools and consolidated workflows | Domain | ||
| SMAGEXP | Container | SMAGEXP (Statistical Meta-Analysis for Gene EXPression) provides a unified way to carry out meta-analysis of gene expression data, while taking care of their specificities. | Tools | ||
| SNIC Science Cloud (SSC) | Academic | A national-scale cloud infrastructure for Swedish Academia | Genomics | ||
| South Green | Server | Genomic resource analysis of southern and Mediterranean plants. | Domain | ||
| Street Science | Server | a Galaxy dedicated for the Street Science Community | Genomics | ||
| SymD | Server | a platform for detecting internally symmetric protein structures | Domain | ||
| TGM | Server | The TGM pipeline is a workflow combining tranSMART server, Galaxy Server and MINERVA platform to enable visually-aided exploration, analysis and interpretation of high-throughput translational medicine data. | Domain | ||
| TreeGenes | Server | TreeGenes integrates genotype, phenotype, and environmental data that can be processed for association mapping and landscape genomics, with a focus on forest trees. This functionality is provided by Tripal Galaxy, a module for Tripal that provides seamless support for running Galaxy workflows directly in the site. Users can analyze data provided by TreeGenes or their own. | Domain | ||
| UseGalaxy.be | Server | General purpose genomics Galaxy server | Genomics | ||
| UseGalaxy.eu | Server | The European UseGalaxy server. | UseGalaxy | ||
| UseGalaxy.fr | Server | General purpose genomics Galaxy server | Genomics | ||
| UseGalaxy.no | Server | A central, joint & free Galaxy instance for Norway-based researchers and their collaborators, with ~2000 bioinformatics tools, 200GB short-term storage and project storage on nels.bioinfo.no. | Genomics | ||
| UseGalaxy.org (Main) | Server | The Galaxy Project free public server; biomedical research | UseGalaxy | ||
| UseGalaxy.org.au | Server | The Australian UseGalaxy server. | UseGalaxy | ||
| USMI Galaxy Demonstrator | Server | This Galaxy implementation is meant to demonstrate integration of microbial domain Biological Resource Center (mBRC) catalogues into the bioinformatics data integration environment. | Tools | ||
| VEuPathDB Galaxy | Academic | A free, interactive, web-based platform for large-scale data analysis focused on eukaryotic pathogens. Merges the former VectorBase and EuPathDB servers. | Domain | ||
| Vinther Lab | Server | RNA structure-probing data analysis to improve the prediction of RNA secondary and tertiary structure and allow structural changes to be identified and investigated. | Tools | ||
| VINYL (Variant prIoritizatioN bY survivaL analysis) | Server | A flexible and fully automated system for the functional annotation and prioritization of genetic variants. | Tools | ||
| VirAmp | Server | VirAmp is a web-based semi-de novo fast virus genome assembly pipeline designed for extremely high coverage NGS data. | Domain | ||
| Virology | Server | A comprehensive set of analysis tools and consolidated workflows for virology work, including SARS-CoV-2. | Domain | ||
| Wageningen UR | Server | Includes microarray tools, the MUMmer suite, and many conversion tools. Strong focus on multi-omics: next to genomics tools it also contains proteomics and metabolomics tools | Tools | ||
| Workflow4Metabolomics | Server | Container | A collaborative portal dedicated to metabolomics data processing, analysis and annotation. | Domain | |
| wQAP | Server | QAP is an open source software that can be used to analyze virus quasispecies using CBS, NGS and TGS data. wQAP (web QAP), is the online version of QAP. | Tools |
Public Servers
Public Servers are acccessible to (at least) any academic researcher in the world. Some require you to create/request an account, aand they may have restrictive quotas, but often, to use these, just go the website and start running analyses. These are free to use.
The folks are Freiburg have put together a public Galaxy server dashboard to track the status and some of the supported features of the servers listed here. See the blog post for more info.
| Resource | Link | Summary | Keywords |
|---|---|---|---|
| AB-OpenLab | Server | FROG stands for FingeRprinting Ontology of Genomic variations. FROG fingerprints have been devised to capture genomic variations at various levels. | Tools |
| ABiMS | Server | Analysis and bioinformatics for Marine Science. | Genomics |
| AGEseq @ AspenDB | Server | This site provides a user-friendly interface for AGEseq (Analysis of Genome Editing by Sequencing) in a Galaxy instance. | Tools |
| ANASTASIA | Server | Automated Nucleotide Aminoacid Sequences Translational plAtform for Systemic Interpretation and Analysis | Genomics |
| APOSTL | Server | Automated Processing of SAINT Templated Layouts (APOSTL) is a freely available software suite and analysis pipeline for reproducible, interactive analysis of AP-MS data. | Tools |
| ARGA | Server | Antibiotic Resistance Gene Analyzer | Domain |
| ARGs-OAP | Server | Fast annotation and classification of antibiotic resistance gene-like sequences from metagenomic data. | Domain |
| ARIAweb | Server | Automated NOE assignment and NMR structure calculation | Domain |
| ARIES | Server | Analysis of genomic data in the field of public health and food safety, with the aim of deploying a comprehensive bioinformatics approach to the study of food-borne zoonoses and infectious diseases at the human and animal interface. | Domain |
| BF2I-MAP | Server | Locally developed as well as standard tools are available on a 16-core server with 32GB memory, accessible to all users, and located in the BF2I lab. | Tools |
| BioBix | Server | A general genomics server. Includes the PROTEOFORMER pipeline tools. | Genomics |
| BioCiphers Lab Galaxy | Server | BCL Galaxy gives a user friendly interface for analysis tools developed by the BioCiphers Lab at the University of Pennsylvania. | Tools |
| BioCompute Object Galaxy | Server | BioCompute Objects is a standard for communication of High-throughput Sequencing (HTS) analysis results, data set creation and curation, and bioinformatics verification protocols. | Genomics |
| BioDivine Toolset | Server | Systems biology tools implemented by the Sybila team. | Tools |
| BioMaS | Server | Taxonomic studies of environmental microbial communities | Tools |
| Biomina | Server | A general purpose Galaxy instance that includes most standard tools for DNA/RNA sequencing, plus extra tools for panel resequencing, variant annotation and some tools for Illumina SNParray analysis. | Genomics |
| BIPAA (BioInformatics Platform for Agroecosystem Arthropods) | Server | Insect genomics (aphids, parasitoïd wasps, lepidopterans) | Domain |
| BitLAB | Server | Detailed analysis of metagenomes. | Tools |
| BRIDGE | Server | Prepare, simulate and analyse and visualise molecular simulations, especially molecular dynamics and free energies. | Domain |
| CAFU | Server | A Galaxy framework for exploring unmapped RNA-Seq data | Domain |
| CBiB Galaxy | Server | A general purpose Galaxy instance that includes EMBOSS (a software analysis package for molecular biology) and fibronectin (diversity analysis of synthetic libraries of a Fibronectin domain). | Genomics |
| CellOrganizer for Galaxy | Server | Create generative models of the spatial organization of cells from microscope images and automatically provide geometries for spatial simulations of cell processes and behaviors | Tools |
| Center for Phage Technology (CPT) | Server | Phage biology and automated annotation. | Domain |
| ChemFlow | Server | Chemometrics without programming: infrared spectrometry on a Galaxy platform. | Domain |
| Chemical Annotation Retrieval Toolkit (CART) | Server | Retrieves annotations on biological effects of chemicals and determines which ones are enriched. | Tools |
| ChemicalToolbox | Server | For processing, analysing and visualising chemical data, and performing molecular simulations. | Domain |
| CIRM-CFBP | Server | Web based access to tools (SkIf, KI-S) of IRHS-EmerSys lab. | Tools |
| Cistrome Analysis Pipeline | Server | ChIP-chip/seq and gene expression data | Domain |
| Climate Science Workbench | Server | A comprehensive set of analysis tools and consolidated workflows for climate analysis and visualisation | Domain |
| CLIP-Explorer | Server | The CLIP-Explorer is a webserver to process, analyse and visualise CLIP-Seq data. | Domain |
| Codon Harmonizer | Server | Easily generate codon harmonized variants of gene sequences for heterologous expression | Tools |
| Coloc-stats | Server | a unified web interface to perform co-localization analysis of genomic features | Domain |
| CoralSNP | Server | Standard Tools for Acroporid Genotyping (STAG) | Domain |
| CorGAT | Server | Align complete assemblies of SARS-CoV-2 genomes wih the reference genomic sequence, to obtain a list of polymorphic positions and to annotate genetic variants. | Domain |
| CoSSci | Server | Tools for solving Galton's problem in Comparative Research and complex network problems in Social Science. | Domain |
| COVID-19 | Server | A companion to our study describing the analysis of early COVID-19 data | Domain |
| deepTS | Server | Explore transcriptional switches from pairwise, temporal, and population RNA-Seq using deepTS. | Tools |
| Dintor | Server | GWA and NGS tools and modules for functional annotation of genes and gene products | Domain |
| epiGeEC | Server | Compare user-provided epigenomic datasets with thousands of public datasets. | Tools |
| Erasmus MC | Server | General purpose genomics analysis, featuring many standard tools plus many additional tools. | Genomics |
| Excellence in Breeding | Server | Hosts tools for the GOBii project, HTPG project and EiB platform, including genomic selection, marker selection, GWAS, imputation, file conversion, and cluster analysis. | Tools |
| FreeBioinfo | Server | Galaxy for metagenomic analysis. | Domain |
| GalaxEast | Server | Integrative 'omics data analysis | Genomics |
| Galaxy Africa | Server | Devoted to assisting researchers on the African continent accelerate their genomics research and analyses. | Genomics |
| Galaxy for Ecology | Server | A web platform to get, process, analyze and visualize ecological data | Domain |
| Galaxy Genome Annotation (GGA) | Server | Galaxy for genome annotation | Domain |
| Galaxy Imaging | Server | Galaxy Docker repository for image analysis | Domain |
| Galaxy Integrated Omics (GIO) | Server | Proteomics Informed by Transcriptomics (PIT) methodology, and selection of surrogate peptides for targeted proteomics. | Domain |
| Galaxy Test | Server | Beta version of Galaxy Main | Genomics |
| Galaxy-P | Server | Galaxy-P is a multiple 'omics' data analysis platform with particular emphasis on mass spectrometry based proteomics. Galaxy-P is developed at the University of Minnesota, deployed at the Minnesota Supercomputing Institute. | Domain |
| Galaxy-SynBioCAD | Server | Synthetic biology and metabolic engineering | Domain |
| Galaxy@GenOuest | Server | A general purpose Galaxy server Includes tools developped by Dyliss and GenScale bioinformatics research teams in Rennes, France. | Genomics |
| Galaxy@Pasteur | Server | General purpose genomics analysis server. | Genomics |
| Galaxy@PRABI | Server | Includes bioinformatics tools developed by the research teams working in the perimeter of the PRABI core facility, including kissplice/kissDE, TETools, SEX-DETector, and priam. | Genomics |
| GalaxyTrakr | Server | Supporting food-borne pathogen research | Domain |
| GASLINI | Server | Supports PIPE-T, a tool for Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) analysis. | Tools |
| GCAC : Galaxy for Compound Activity Classification | Server | GCAC is a web enabled platform for predictive model building using R and caret package for virtual screening. | Tools |
| GeneLab | Server | NASA GeneLab is a comprehensive space-related omics database in which users can upload, download, share, store, and analyze spaceflight and corresponding model organism data. | Genomics |
| Genomic Hyperbrowser | Server | Statistical methodology and computing power to handle a variety of biological inquires on genomic datasets | Domain |
| GigaGalaxy | Server | GigaGalaxy hosts tools and data analyses from papers published in *GigaScience*. | Genomics |
| GraphClust | Server | GraphClust2 is a workflow for scalable clustering of RNAs based on sequence and secondary structures feature. GraphClust2 is implemented within the Galaxy framework and consists a set of integrated Galaxy tools and flavors of the linear-time clustering workflow. | Tools |
| GrAPPA | Server | GrAPPA is a web-based interface constructed on the Galaxy framework for graph theoretical tools. It contains novel combinatorial methods integrated into a complete microarray analysis toolchain, from uploading raw high-throughput data to visualization of results. | Domain |
| Halogen Bonding | Server | Visualize halogen bond contacts in the protein binding site. Analyze a protein binding site for halogen bonding hotspots. Evaluate halogen contacts with the protein backbone using the scoring function XBScore. | Tools |
| Hardwood Genomics | Server | A simplified, workflow-centic interface to Galaxy, focused on genomics data from hardwood trees. | Domain |
| HiCExplorer | Server | Tools to process and visualize chromosome conformation. | Domain |
| Human Cell Atlas | Server | Tools and workflows for the analysis of Single Cell RNA-Seq data. It includes a module that connects to the Matrix Service API of the Human Cell Atlas’s Data Coordination Platform that enables retrieval of gene expression matrices from any data sets in the Human Cell Atlas. | Domain |
| Huttenhower Lab | Server | metagenomic and functional genomic analyses, intended for research and academic use | Domain |
| HyPhy HIV NGS Tools | Server | Tools for HIV sequencing analysis. | Domain |
| IBERS @ Aberystwyth | Server | Software, tools and pages written by IBERS researchers for release to the wider community. | Tools |
| IDENAP | Server | Inter-Domain Ecological Network Analysis Pipeline | Domain |
| Image Analysis and Processing Toolkit | Server | Image analysis and processing. | Domain |
| ImmPort Galaxy | Server | Flow Cytometry Analysis. | Domain |
| immuneML | Server | Machine learning-based analysis and classification of adaptive immune receptors and repertoires (AIRR). | Domain |
| InteractoMIX | Server | A one-stop resource offering a wide range of computational analyses from proteome-wide interactomes to structure of protein complexes | Domain |
| IPK Galaxy Blast Suite | Server | Part of the IPK Crop Analysis Tools Suite (CATS). Offers access to genomic references published by IPK and collaborative projects | Domain |
| Langille Lab | Server | Prediction of the unobserved character states in a community of organisms from phylogenetic information. | Tools |
| LAPPS Grid | Server | An open, interoperable web service platform for natural language processing (NLP) research and development. | Domain |
| Lebanese University Galaxy | Server | Includes the SpCLUST tool set for fast and reliable clustering of potentially divergent biological sequences | Tools |
| Lifeportal | Server | a Galaxy instance to satisfy the computational needs of the Norwegian research community in life sciences but also of any other user willing to use the service. | Genomics |
| LiSIs | Server | A platform for Virtual Screening. | Tools |
| Machine Learning Workbench | Server | A comprehensive set of data preprocessing, machine learning, deep learning and visualisation tools, consolidated workflows for end-to-end machine learning analysis and training materials to showcase the usage of these tools. | Domain |
| Majewski Lab | Server | Detection of recurrent Allelic Imbalance in tumors using whole Exome sequencing data. | Tools |
| Mandoiu Lab | Server | A customized installation of the Galaxy framework deploying bioinformatic tools and pipelines developed in the Mandoiu Lab at the University of Connecticut for high-throughput sequencing and immunogenomics data analysis | Tools |
| MaREA4Galaxy | Server | Metabolic Reaction Enrichment Analysis and visualization of RNA-seq data | Tools |
| Martin Luther U. Halle-Wittenberg | Server | Provides implementations of GeMoMa, InMoDe, CRISPRer, TALgetter, TALgetterLong, TALENoffer, and Dimont | Tools |
| Metabolomics | Server | A community driven metabolomics Galaxy service | Domain |
| Metagenomics | Server | a webserver to process, analyse and visualize Metagenomic and Microbiota data in general. | Domain |
| Metaproteomics Gateway | Server | Metaproteomics gateway providing access to documentation and other instructional materials, and an opportunity for hands-on training using example datasets and optimized metaproteomics workflows | Domain |
| Migale | Server | A general purpose genomics server with an emphasis on metagenomics, including FROGS and several Migale developed tools. | Genomics |
| MiModD NacreousMap | Server | NacreousMap mapping/plotting tool of MiModD for users of MiModD who do not want to install the required dependencies (R and rpy2) for graphical output from this tool on their local system. | Tools |
| MISSISSIPPI | Server | Support for analyses of RNA and small RNA sequencing datasets as well as for epigenetics or metagenomics studies. | Domain |
| Molecular Property Diagnostic Suite - Diabetes Mellitus Portal (MPDSDM) | Server | A disease-specific open source web portal for Diabetes Mellitus. | Domain |
| Molecular Property Diagnostic Suite - Tuberculosis (MPDSTB) | Server | A disease-specific web portal for Tuberculosis for drug discovery and development. | Domain |
| NanoGalaxy | Server | a webserver to process, analyse and visualize Oxford Nanopore Technologies (ONT) data and similar long-reads technologies. | Domain |
| NetworkAnalyst | Server | For mapping and quantification of raw RNA-seq data | Domain |
| NG-Tax | Server | A Semantic Framework for High-throughput Marker Gene (Amplicon) Analysis | Tools |
| NGPhylogeny.fr | Server | Robust phylogenetic analysis for everyone. | Domain |
| Oqtans | Server | Customized Galaxy, extended with machine learning based tools for sequence and tiling array data analysis. | Domain |
| Orione | Server | A Galaxy based web server for microbiology. Orione includes all post mapping or assembling steps from scaffolding to complete annotation pipelines. | Domain |
| OSDDlinux LiveGalaxy | Server | Drug discovery | Domain |
| Osiris | Server | Phylogenetics | Tools |
| Palfinder | Server | Microsatellite development. | Tools |
| PepSimili | Server | Integrated workflow tool for mapping of massive peptide repertoires on whole proteomes and delivering streamlined, systems-level biological interpretation. | Tools |
| PhagePromotor | Server | Predict promoter sequences in phage genomes, using machine learning models. | Tools |
| PIA | Server | Phylogenetics and gene interaction | Tools |
| Plant Anaylsis Workbench | Server | A community driven plant data analsys Galaxy service | Domain |
| PlantGenIE | Server | Plant Genome Integrative Explorer Galaxy instance | Domain |
| PreSTIGE | Server | Predicting Specific Tissue Interactions of Genes and Enhancers | Tools |
| Proteogenomics Gateway | Server | Provides access to documentation and other instructional materials, and an opportunity for hands-on training using example datasets and optimized proteogenomics workflows. The main goal of this server is to provide documentation to facilitate training and mastery of these software and workflows. | Domain |
| ProteoRE | Server | ProteoRE (Proteomics Research Environment) | Domain |
| Protologger | Server | All-in-one genome description tool, aimed at simplifying gathering the data required for writing protologues. This includes providing taxonomic, functional and ecological insights. | Tools |
| RepeatExplorer | Server | Graph-based clustering and characterization of repetitive sequences, and detection of transposable element protein coding domains. | Domain |
| RiboGalaxy | Server | Tools for the analysis and visualization of ribo-seq data obtained with the ribosome profiling technique. | Domain |
| Rice Galaxy | Server | Tools for designing single-nucleotide polymorphism assays, analyzing genome-wide association studies, population diversity, rice−bacterial pathogen diagnostics, and a suite of published genomic prediction methods. | Domain |
| RNA Workbench | Server | more than 50 bioinformatics tools dedicated to different research areas of RNA biology, including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-Seq analysis, and RNA target prediction. | Domain |
| Sciensano | Server | General purpose Galaxy server optimized for microbiological genomics applications of interest for public health. | Genomics |
| Single Cell Omics workbench | Server | The Single Cell Omics workbench is a comprehensive set of analysis tools and consolidated workflows | Domain |
| South Green | Server | Genomic resource analysis of southern and Mediterranean plants. | Domain |
| Street Science | Server | a Galaxy dedicated for the Street Science Community | Genomics |
| SymD | Server | a platform for detecting internally symmetric protein structures | Domain |
| TGM | Server | The TGM pipeline is a workflow combining tranSMART server, Galaxy Server and MINERVA platform to enable visually-aided exploration, analysis and interpretation of high-throughput translational medicine data. | Domain |
| TreeGenes | Server | TreeGenes integrates genotype, phenotype, and environmental data that can be processed for association mapping and landscape genomics, with a focus on forest trees. This functionality is provided by Tripal Galaxy, a module for Tripal that provides seamless support for running Galaxy workflows directly in the site. Users can analyze data provided by TreeGenes or their own. | Domain |
| UseGalaxy.be | Server | General purpose genomics Galaxy server | Genomics |
| UseGalaxy.eu | Server | The European UseGalaxy server. | UseGalaxy |
| UseGalaxy.fr | Server | General purpose genomics Galaxy server | Genomics |
| UseGalaxy.no | Server | A central, joint & free Galaxy instance for Norway-based researchers and their collaborators, with ~2000 bioinformatics tools, 200GB short-term storage and project storage on nels.bioinfo.no. | Genomics |
| UseGalaxy.org (Main) | Server | The Galaxy Project free public server; biomedical research | UseGalaxy |
| UseGalaxy.org.au | Server | The Australian UseGalaxy server. | UseGalaxy |
| USMI Galaxy Demonstrator | Server | This Galaxy implementation is meant to demonstrate integration of microbial domain Biological Resource Center (mBRC) catalogues into the bioinformatics data integration environment. | Tools |
| Vinther Lab | Server | RNA structure-probing data analysis to improve the prediction of RNA secondary and tertiary structure and allow structural changes to be identified and investigated. | Tools |
| VINYL (Variant prIoritizatioN bY survivaL analysis) | Server | A flexible and fully automated system for the functional annotation and prioritization of genetic variants. | Tools |
| VirAmp | Server | VirAmp is a web-based semi-de novo fast virus genome assembly pipeline designed for extremely high coverage NGS data. | Domain |
| Virology | Server | A comprehensive set of analysis tools and consolidated workflows for virology work, including SARS-CoV-2. | Domain |
| Wageningen UR | Server | Includes microarray tools, the MUMmer suite, and many conversion tools. Strong focus on multi-omics: next to genomics tools it also contains proteomics and metabolomics tools | Tools |
| Workflow4Metabolomics | Server | A collaborative portal dedicated to metabolomics data processing, analysis and annotation. | Domain |
| wQAP | Server | QAP is an open source software that can be used to analyze virus quasispecies using CBS, NGS and TGS data. wQAP (web QAP), is the online version of QAP. | Tools |
Academic Cloud Services
These are academic cloud providers where ready to run Galaxy instances are available. Many of these are restricted to users within a particular geographic domain, for example, a country, province, or consortium of countries. These are often free to eligible researchers.
| Resource | Link | Summary | Purview | Keywords |
|---|---|---|---|---|
| AnVIL | Academic | Run Galaxy inside the secure AnVIL environment on Google Cloud Platform. | Global | Genomics |
| CLIMB | Academic | The CLIMB project (Cloud Infrastructure for Microbial Bioinformatics) develops and deploys a world leading cyber-infrastructure for microbial bioinformatics; providing free cloud-based compute, storage, and analysis tools for academic microbiologists in the UK. | United Kingdom | Genomics |
| GenAP | Academic | All Canadian researchers are eligible for a GenAP account. International researchers that have a Canadian collaborator can also be sponsored and become eligible to a GenAP account as well. | Canada | Genomics |
| Globus Genomics | Academic | Globus Genomics provides hardened high-performance Galaxy servers running with Globus on AWS. | Global | Genomics |
| Jetstream | Academic | Jetstream is part of XSEDE, a "collection of integrated advanced digital resources and services" and is funded by NSF. | United States | Genomics |
| Laniakea | Academic | Laniakea provides the possibility to automate the creation of Galaxy-based virtualized environments through an easy setup procedure, providing an on-demand workspace ready to be used by life scientists and bioinformaticians, with built-in storage encryption for user data. | Italy | Genomics |
| MetaCentrum | Academic | MetaCentrum regional virtual organization of the Czech National Grid Infrastructure (NGI) and is accessible to employees and students of research and academic organizations of the Czech Republic and for scientific purposes only. | Czechia | Genomics |
| Nectar Cloud | Academic | Set up a Galaxy server on Australia's Nectar research cloud. | Australia | Genomics |
| PhenoMeNal | Academic | Large scale computing for medical informatics | Domain | |
| SNIC Science Cloud (SSC) | Academic | A national-scale cloud infrastructure for Swedish Academia | Sweden | Genomics |
| VEuPathDB Galaxy | Academic | A free, interactive, web-based platform for large-scale data analysis focused on eukaryotic pathogens. Merges the former VectorBase and EuPathDB servers. | Global | Domain |
Commercial Cloud Services
These are commercial cloud providers where ready to run Galaxy instances are available. You need to pay for these, but you only need to pay for as long as you need the instance to be up.
| Resource | Link | Summary | Keywords |
|---|---|---|---|
| Amazon Web Services (AWS) | Commercial | Set up you own general purpose genomics server runing AWS using GVL and CloudMan. | Genomics |
| AnVIL | Commercial | Run Galaxy inside the secure AnVIL environment on Google Cloud Platform. | Genomics |
| G-OnRamp | Commercial | G-OnRamp provides a user-friendly, web-based platform for collaborative, end-to-end annotation of eukaryotic genomes using UCSC Assembly Hubs and JBrowse/Apollo genome browsers with evidence tracks derived from sequence alignments, ab initio gene predictors, RNA-Seq data, and repeat finders. | Domain |
| Globus Genomics | Commercial | Globus Genomics provides hardened high-performance Galaxy servers running with Globus on AWS. | Genomics |
| PhenoMeNal | Commercial | Large scale computing for medical informatics | Domain |
Containers
These Galaxy instances are prepackaged using container technology, usually Docker. You run these locally by first installing the container technology (Docker is easy), and then launching the containerized Galaxy within that technology. These use local resources.
| Resource | Link | Summary | Keywords |
|---|---|---|---|
| ASaiM | Container | Integrates tools specifically chosen for metagenomic and metatranscriptomic studies and hierarchically organized to orient user choice toward the best tool for a given task. | Tools |
| ATACgraph | Container | ATAC-seq for biologists with minimal bioinformatics knowledge to analyze chromatin accessibility | Domain |
| BRIDGE | Container | Prepare, simulate and analyse and visualise molecular simulations, especially molecular dynamics and free energies. | Domain |
| CAFU | Container | A Galaxy framework for exploring unmapped RNA-Seq data | Domain |
| ChemicalToolbox | Container | For processing, analysing and visualising chemical data, and performing molecular simulations. | Domain |
| CRAVAT-P | Container | A Docker image containing a fully-operational Galaxy instance with pre-installed demonstration material for CRAVAT-P. | Tools |
| deepTS | Container | Explore transcriptional switches from pairwise, temporal, and population RNA-Seq using deepTS. | Tools |
| DocMethyl EpiMOLAS | Container | Galaxy Docker for DNA methylation analysis in WGBS | Domain |
| Epigenomics Galaxy | Container | Galaxy Docker image for epigenomics analysis | Domain |
| EWAS-Galaxy | Container | Galaxy Docker image for population epigenetics data analysis | Domain |
| Galaxy basic sequence manipulation | Container | Galaxy Docker repository for basic sequence data analysis. | Domain |
| Galaxy BLAST+ | Container | A complete and production ready Galaxy instance with installed BLAST+ tools. | Domain |
| Galaxy Docker | Container | The Galaxy Docker Image is an easy distributable full-fledged Galaxy installation, that can be used for testing, teaching and presenting new tools and features. | Genomics |
| Galaxy Exome-Seq | Container | Galaxy Docker repository for Exome sequencing data analysis | Domain |
| Galaxy Genome Annotation (GGA) | Container | Galaxy for genome annotation | Domain |
| Galaxy Imaging | Container | Galaxy Docker repository for image analysis | Domain |
| Galaxy mothur Toolset Docker | Container | Galaxy Docker image for microbial ecology analysis with mothur | Domain |
| Galaxy Workbench for Mass Spectrometry Imaging | Container | Galaxy Docker image for mass spec imaging | Domain |
| GraphClust | Container | GraphClust2 is a workflow for scalable clustering of RNAs based on sequence and secondary structures feature. GraphClust2 is implemented within the Galaxy framework and consists a set of integrated Galaxy tools and flavors of the linear-time clustering workflow. | Tools |
| MGS-Fast | Container | Shotgun whole-genome metagenomic analysis using DNA-DNA alignment | Domain |
| miCloud | Container | Leverage cloud technologies to provide an easy-to-use streamlined NGS data analysis using local computational hardware | Genomics |
| NG-Tax | Container | A Semantic Framework for High-throughput Marker Gene (Amplicon) Analysis | Tools |
| NGPhylogeny.fr | Container | Robust phylogenetic analysis for everyone. | Domain |
| q2Galaxy | Container | QIIME 2 Galaxy Docker image. | Tools |
| QuanTP | Container | A Docker image containing a fully-operational Galaxy instance with pre-installed QuanTP tools. | Tools |
| RiboGalaxy | Container | Tools for the analysis and visualization of ribo-seq data obtained with the ribosome profiling technique. | Domain |
| RNA Modification Calling | Container | Galaxy Docker image for RNA analysis and modification calling | Tools |
| RNA Workbench | Container | more than 50 bioinformatics tools dedicated to different research areas of RNA biology, including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-Seq analysis, and RNA target prediction. | Domain |
| SARS-CoV-2 ENA Submission | Container | Galaxy Docker image for submitting SARS-CoV-2 data to ENA | Tools |
| SMAGEXP | Container | SMAGEXP (Statistical Meta-Analysis for Gene EXPression) provides a unified way to carry out meta-analysis of gene expression data, while taking care of their specificities. | Tools |
| Workflow4Metabolomics | Container | A collaborative portal dedicated to metabolomics data processing, analysis and annotation. | Domain |
Virtual Machines (VMs)
VMs are similar to containers but use a different technology. Containers take significant advantage of your computer's underlying operating system. Virtual Machines include an entire supporting operating system, and are significantly larger than containers. You run these locally by first installing a VM player like VirtualBox, and then downloading and launching the VM within that player. These use local resources.
| Resource | Link | Summary | Keywords |
|---|---|---|---|
| G-OnRamp | VM | G-OnRamp provides a user-friendly, web-based platform for collaborative, end-to-end annotation of eukaryotic genomes using UCSC Assembly Hubs and JBrowse/Apollo genome browsers with evidence tracks derived from sequence alignments, ab initio gene predictors, RNA-Seq data, and repeat finders. | Domain |
| GCAC : Galaxy for Compound Activity Classification | VM | GCAC is a web enabled platform for predictive model building using R and caret package for virtual screening. | Tools |
| PiRATE: a Pipeline to Retrieve and Annotate Transposable Elements | VM | Detect, classify and annotate TEs of non-model organisms. | Tools |
| Shapiro Lab | VM | RNA structure and design tools including RNA2D3D and StructureLab | Tools |
About This Directory
The Galaxy Community has created Galaxy instances in many different forms and for many different applications. This directory lists the options we know about, including:
- Galaxy servers,
- cloud services that support Galaxy instances, and
- virtual machines and containers that can be easily deployed for your own server.
Which Platform / Platform Type to Choose?
Your choices depends upon your needs. If you want to use Galaxy with a minimum of setup work, then try starting with a UseGalaxy orPublic Server. There are over 125 of these platforms to pcik from all of which can be use with little or no setup on your part. However if none of those meet your needs then here are some guidelines for other cases.
| UseGalaxy Servers | Public Servers | TIaaS | Academic Clouds | Commercial Clouds | Containers | VMs | Local | |
|---|---|---|---|---|---|---|---|---|
| Free to use | Yes | Yes | Yes | Yes1 | No | Yes | Yes | Yes |
| Uses your local compute infrastructure | No | No | No | No | No | Yes2 | Yes2 | Yes |
| Datasets (including intermediate) total > 250GB | No | ?5 | Yes | Yes | Yes | Yes3 | Yes3 | Yes |
| Computational requirements are similarly large | No | ?5 | Yes | Yes | Yes | Yes3 | Yes3 | Yes |
| Share Galaxy objects outside your organization | Yes | Yes | Yes | Yes | Yes | Yes4 | Yes4 | Yes5 |
| Install custom tools and reference genomces | No | No | No | Yes5 | Yes | Yes | Yes | Yes |
| Have absolute data security requirements | No | No | No | ?5 | ?5 | ?5 | ?5 | Yes |
1 Depends on provider, and if you are eligible for the service
2 These technologies can be deployed on clouds or locally.
3 Depends on the size of the system you are running it on.
4 With these technologies you can save the server and share the entire platform with them.
5 Depends on configuration.
Most of these platform types are defined above (click on each tab), but two aren't:
TIaaS
Training Infrastructure as a Service (TIaaS) is a service offered by some UseGalaxy servers to specifically support training use cases. See TIaaS for more information.
Local
Finally, you can install your own local instance of Galaxy from scratch. See Get Galaxy for details on how to do this. This has become much easier to do in recent years.
Resource Keywords
Each resource has a set of keywords associated with them.
Real keywords
(What about listing these by the resource's domain, for example, the research methodology (e.g., RNA-Seq), the clade (e.g., crops), or field e.g., metagenomics) that a resource is targeted at? We are working on it.)Scope
Initially, there is only one keyword per resource and that defines the scope of the resource:
UseGalaxy
UseGalaxy servers implement a common core set of tools and reference genomes, and are open to anyone to use.
Genomics
These servers implement a broad range of tools and aren't specific to any part of the tree of life, or to any type of analysis.
Domain
Domain resources specialize in either a particular branch of the tree of life or in particular types of analysis. Within their specializations, domain resources offer a wide variety of tools.
Tool Publishing
Tool publishing resources make tools easily available so that researchers can use them without having to install and use command line versions. The distinction between domain resources and tool publishing resources is fuzzy. In general, tool publishing resources expose tools from a particular organization, while domain resources include tools / datasets from other organizations and have a larger goal in mind.
Add a resource to this directory
If you maintain a Galaxy resource that can be listed on this directory, then please describe your Galaxy resource here. We'll contact you with any question and then post it this directory.