Galaxy Platform Directory: Servers, Clouds, and Deployable Resources

125+ platforms to use Galaxy on


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.

ResourceServerSummaryKeywords
UseGalaxy.euServerThe European UseGalaxy server. UseGalaxy
UseGalaxy.org (Main)ServerThe Galaxy Project free public server; biomedical research UseGalaxy
UseGalaxy.org.auServerThe Australian UseGalaxy server. UseGalaxy

Complete listing of resources for using Galaxy.

ResourceServerCloudDeploy- ableSummaryKeywords
A-GameServerA Galaxy suite for tArgeted MEtagenomics Domain
AB-OpenLabServerFROG stands for FingeRprinting Ontology of Genomic variations. FROG fingerprints have been devised to capture genomic variations at various levels. Tools
ABiMSServerAnalysis and bioinformatics for Marine Science. Genomics
ABiMS-ToolsServerHosts tools/resources developed at the Station Biologique de Roscoff in collaboration with ABiMS. Tools
AGEseq @ AspenDBServerThis site provides a user-friendly interface for AGEseq (Analysis of Genome Editing by Sequencing) in a Galaxy instance. Tools
Alveo: Human Communication Science Virtual Laboratory ServerHuman Communication Science (HCS). Domain
Amazon Web Services (AWS)CommercialSet up you own general purpose genomics server runing AWS using GVL and CloudMan. Genomics
ANASTASIAServerAutomated Nucleotide Aminoacid Sequences Translational plAtform for Systemic Interpretation and Analysis Genomics
Antigen Receptor Galaxy (ARGalaxy)ServerAutomate the analysis and visual reporting of T- and B-cell receptor repertoire sequencing data. Tools
APOSTLServerAutomated Processing of SAINT Templated Layouts (APOSTL) is a freely available software suite and analysis pipeline for reproducible, interactive analysis of AP-MS data. Tools
ARGs-OAPServerFast annotation and classification of antibiotic resistance gene-like sequences from metagenomic data. Tools
ARIESServerAnalysis 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
ballaxyContainerHosts the BALL (Biochemical Algorithms Library) Project tools, i.e. computer aided drug design and molecular modelling based on protein and ligand structure data. Domain
BF2I-MAPServerLocally 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
BioBixServerA general genomics server. Includes the PROTEOFORMER pipeline tools. Genomics
BioCiphers Lab GalaxyServerBCL Galaxy gives a user friendly interface for analysis tools developed by the BioCiphers Lab at the University of Pennsylvania. Tools
BioMaSServerTaxonomic studies of environmental microbial communities Tools
BiominaServerA 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)ServerInsect genomics (aphids, parasitoïd wasps, lepidopterans) Domain
BitLABServerDetailed analysis of metagenomes. Tools
CBiB GalaxyServerA 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
Center for Phage Technology (CPT)ServerPhage biology and automated annotation. Domain
ChemFlowServerChemometrics without programming: infrared spectrometry on a Galaxy platform. Domain
Chemical Annotation Retrieval Toolkit (CART)ServerRetrieves annotations on biological effects of chemicals and determines which ones are enriched. Tools
ChimeRScopeServerFusion gene discovery from transcriptome-sequencing (RNA-seq) datasets. Tools
Cistrome Analysis PipelineServerChIP-chip/seq and gene expression data Domain
CLIMBAcademicThe 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
Codon HarmonizerServerEasily generate codon harmonized variants of gene sequences for heterologous expression Tools
CoSSciServerTools for solving Galton's problem in Comparative Research and complex network problems in Social Science. Domain
CRAVAT-PContainerA Docker image containing a fully-operational Galaxy instance with pre-installed demonstration material for CRAVAT-P. Tools
DBCLS GalaxyServerAdds text mining tools, DBCLS DBSearch Tools, semantic web tools Genomics
DDBJ Read Annotation PipelineVMAnnotates raw sequencing reads from next-generation sequencers(NGS) with high throughput, which are registered in DDBJ Read Archive (DRA). Tools
deepToolsServerContainerdeepTools is a suite of user-friendly tools for the visualization, quality control and normalization of data from high-throughput DNA sequencing experiments. Tools
DintorServerGWA and NGS tools and modules for functional annotation of genes and gene products Domain
EGI MarketplaceAcademicGalaxy instances on a European wide federation of research cloud providers. Genomics
epiGeECServerCompare user-provided epigenomic datasets with thousands of public datasets. Tools
EpiToolKitServerComputational immunology for the development of novel epitope-based vaccines. Tools
Erasmus MCServerGeneral purpose genomics analysis, featuring many standard tools plus many additional tools. Genomics
EuPathDB GalaxyAcademicA free, interactive, web-based platform for large-scale data analysis focused on eukaryotic pathogens. Domain
GalaxEastServerIntegrative 'omics data analysis Genomics
Galaxy basic sequence manipulationContainerGalaxy Docker repository for basic sequence data analysis. Domain
Galaxy BLAST+ContainerA complete and production ready Galaxy instance with installed BLAST+ tools. Domain
Galaxy ChIP-Seq DockerContainerGalaxy Docker image for ChipSeq analysis Domain
Galaxy CSGContainerGalaxy instance with tools for Constructive Solid Geometry shipped in a Docker container. Domain
Galaxy DockerContainerThe 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-SeqContainerGalaxy Docker repository for Exome sequencing data analysis Domain
Galaxy Genome AnnotationContainerGalaxy Docker repository for genome annotation Domain
Galaxy ImagingContainerGalaxy Docker repository for image analysis Domain
Galaxy Integrated Omics (GIO)ServerProteomics Informed by Transcriptomics (PIT) methodology, and selection of surrogate peptides for targeted proteomics. Domain
Galaxy PGTB (Virtual Biodiversity Lab)ServerThis is a standard Galaxy instance implemented with specific tools for Biodiversity (Biodiversity Virtual Lab) and NGS (Ion Torrent from the PGTB facility) analysis. Domain
Galaxy TestServerBeta version of Galaxy Main Genomics
Galaxy-CEFAPServerGalaxy-CEFAP offers a set of tools to perform RNA-Seq and miRNA analysis. Domain
Galaxy-PServerGalaxy-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@GenOuestServerA general purpose Galaxy server Includes tools developped by Dyliss and GenScale bioinformatics research teams in Rennes, France. Genomics
Galaxy@PasteurServerGeneral purpose genomics analysis server. Genomics
Galaxy@PRABIServerIncludes 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
GenAPAcademicAll 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
GeneLabServerNASA 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 HyperbrowserServerStatistical methodology and computing power to handle a variety of biological inquires on genomic datasets Domain
GigaGalaxyServerGigaGalaxy hosts tools and data analyses from papers published in *GigaScience*. Genomics
Globus GenomicsAcademicGlobus Genomics provides hardened high-performance Galaxy servers running with Globus on AWS. Genomics
GrAPPAServerGrAPPA 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 BondingServerVisualize 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 GenomicsServerA simplified, workflow-centic interface to Galaxy, focused on genomics data from hardwood trees. Domain
Hunter College GalaxyServerA general purpose genomics server Genomics
Huttenhower LabServermetagenomic and functional genomic analyses, intended for research and academic use Domain
IBERS @ AberystwythServerSoftware, tools and pages written by IBERS researchers for release to the wider community. Tools
Image Analysis and Processing ToolkitServerImage analysis and processing. Domain
ImmPort GalaxyServerFlow Cytometry Analysis. Domain
ImmunoGlobulin Galaxy (IGGalaxy)VMProvides a set of tools for easy detection and quantitation of immunoglobulin heavy chain alternative transcripts. Domain
In Silico GalaxyServerConstruction, analysis, and visualization of gene-gene interaction networks for sequencing data. Tools
Insitut CurieServerGeneral purpose genomic Galaxy server. Contains tools for Ion Torrent data, many RNA-Seq tools, ncPRO-seq, RSAT, Nebula tools, copy number and LOH tools, and NGS diagnostic tools. Genomics
International Rice Research Institute (IRRI) GalaxyServerBioinformatics workbench, with rice-specific data (i.e. genomes) and tools (mostly specialized for the IRRI Genotyping Service Laboratory) installed. Domain
IRProfilerServerContainerImmune Repertoire Profiler (IRProfiler), a novel software pipeline that delivers a number of core receptor repertoire quantification and comparison functionalities on high-throughput TR and BcR sequencing data. Tools
JetstreamAcademicJetstream is part of XSEDE, a "collection of integrated advanced digital resources and services" and is funded by NSF. Genomics
kmer-SVMServerTool suite uses a support vector machine (SVM) with kmer sequence features to identify predictive combinations of short transcription factor binding sites which determine the tissue specificity of the original NGS assay. Tools
Koslicki LabServerWeb based access to tools created by the Koslicki Lab at Oregon State University. Tools
KREAPVMKinetic Re-Epithelialization Analysis Pipeline Tools
Langille LabServerPrediction of the unobserved character states in a community of organisms from phylogenetic information. Tools
Laniakea/INDIGO-DataCloudAcademicLaniakea 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 GridServerAn open, interoperable web service platform for natural language processing (NLP) research and development. Domain
LiSIsServerA platform for Virtual Screening. Tools
Majewski LabServerDetection of recurrent Allelic Imbalance in tumors using whole Exome sequencing data. Tools
Martin Luther U. Halle-WittenbergServerProvides implementations of InMoDe, CRISPRer, TALgetter, TALgetterLong, TALENoffer, and Dimont Tools
MBAC Metabiome PortalServerSimplifying control, usage, access, and analysis of microbiome, metabolome, and immunome data (the Metabiome). Tools
MetaCentrumAcademicMetaCentrum 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
Metaproteomics GatewayServerMetaproteomics gateway providing access to documentation and other instructional materials, and an opportunity for hands-on training using example datasets and optimized metaproteomics workflows Domain
MGEScanServerCommercialIdentifying long terminal repeats (LTR) and non-LTR retroelements in eukaryotic genomic sequences. Tools
MiModD NacreousMapServerNacreousMap 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
MISSISSIPPIServerSupport 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)ServerA disease-specific open source web portal for Diabetes Mellitus. Domain
Molecular Property Diagnostic Suite - Tuberculosis (MPDSTB)ServerA disease-specific web portal for Tuberculosis for drug discovery and development. Domain
MPI-HLR Bioinformatics ServerServerHosts the MIRPIPE, ADMIRE, and LimiTT tools Tools
NebulaServerallows users (Bioinformaticians as far as Biologists) to analyze their ChIP-seq data. Domain
Nectar CloudAcademicSet up a Galaxy server on Australia's Nectar research cloud. Genomics
NELLYServerPlataforma de servicios para análisis de datos biomédicos en bioinformática featuring standard Galaxy Tools Genomics
NeLSAcademicLife Science platform for Norwegian academic researchers. Genomics
NGS-QCServerEvaluate the quality of your favorite ChIP-seq or enrichment-related NGS dataset using NGS-QC Generator, which also includes a database with preprocessed profiles and a tutorial on how to analyze sequencing profiles yourself. Tools
OqtansServerCommercialCustomized Galaxy, extended with machine learning based tools for sequence and tiling array data analysis. Domain
OrioneServerA Galaxy based web server for microbiology. Orione includes all post mapping or assembling steps from scaffolding to complete annotation pipelines. Domain
OSDDlinux LiveGalaxyServerDrug discovery Domain
OsirisServerPhylogenetics Tools
PalfinderServerMicrosatellite development. Tools
PhenoMeNalServerLarge scale computing for medical informatics Domain
PIAServerPhylogenetics and gene interaction Tools
PIPE-CLIPServerReliable analysis of data generated by three types of CLIP-seq protocol: HITS-CLIP, PAR-CLIP and iCLIP. Tools
Pitagora-GalaxyServerCommercialVMThe Pitagora-Galaxy Project server intended for testing and sharing. Heavy analysis should be performed using the project's identical virtual machine (VM) or Amazon Machine Image (AMI). Genomics
PL-GridAcademicThe PL-Grid project is free of charge for any Polish scientist. It is also free for any foreign collaborator of Polish scientists. Genomics
PlantGenIEServerPlant Genome Integrative Explorer Galaxy instance Domain
PreSTIGEServerPredicting Specific Tissue Interactions of Genes and Enhancers Tools
Proteogenomics GatewayServerProvides 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
ProteoREServerProteoRE (Proteomics Research Environment) Domain
QBRC GalaxyServerHosts custom tools developed by members of the Quantitative Biomedical Research Center @ University of Texas Southwestern for statistical analysis of various High Throughput Sequencing experiments. Tools
RDF2GraphServerRDF2Graph recovers the structure of an RDF resource. Tools
RepeatExplorerServerGraph-based clustering and characterization of repetitive sequences, and detection of transposable element protein coding domains. Domain
RiboGalaxyServerContainerTools for the analysis and visualization of ribo-seq data obtained with the ribosome profiling technique. Domain
RNA WorkbenchContainermore 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
RNA-Rocket @ Pathogen PortalServerSupports comparative analysis of host response to pathogens. It provides an RNA-Seq pipeline to characterize the transcriptome of all NIAID Bioinformatic Resource Center (BRC) pathogens and their key hosts. Domain
RNAcommenderContainerRNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. It is a recommender system capable of suggesting RNA targets to unexplored RNA binding proteins, by propagating the available interaction information, taking into account the protein domain composition and the RNA predicted secondary structure. Tools
SIFTEDServerSpecificity Inference For TAL-Effector Design (SIFTED) Tools
SMAGEXPContainerSMAGEXP (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)AcademicA national-scale cloud infrastructure for Swedish Academia Genomics
South GreenServerGenomic resource analysis of southern and Mediterranean plants. Domain
SplicescopeServerPrediction of neuronal maturation using splicing profiles Tools
Stem Cell Discovery EngineServerDatabase of curated cancer stem cell experiments coupled to Galaxy. Domain
SymDServera platform for detecting internally symmetric protein structures Domain
UseGalaxy.euServerThe European UseGalaxy server. UseGalaxy
UseGalaxy.org (Main)ServerThe Galaxy Project free public server; biomedical research UseGalaxy
UseGalaxy.org.auServerThe Australian UseGalaxy server. UseGalaxy
USMI Galaxy DemonstratorServerThis Galaxy implementation is meant to demonstrate integration of microbial domain Biological Resource Center (mBRC) catalogues into the bioinformatics data integration environment. Tools
VarCapServerReliable prediction of different types of variants even at low frequencies. Tools
VectorBase GalaxyAcademicA full Galaxy server that includes reference information and workflows focusing on invertebrate vectors of human pathogens. Domain
Vinther LabServerRNA structure-probing data analysis to improve the prediction of RNA secondary and tertiary structure and allow structural changes to be identified and investigated. Tools
VirAmpServerVirAmp is a web-based semi-de novo fast virus genome assembly pipeline designed for extremely high coverage NGS data. Domain
Wageningen URServerIncludes 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
Workflow4MetabolomicsServerContainerA collaborative portal dedicated to metabolomics data processing, analysis and annotation. Domain
ZBIT Bioinformatics ToolboxServerThis customized version of the Galaxy webservice framework was set up to allow the public access of our bioinformatics tools. These tools were developed and implemented by members of the Department of Cognitive Systems at the University of Tübingen. 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.

ResourceLinkSummaryKeywords
A-GameServerA Galaxy suite for tArgeted MEtagenomics Domain
AB-OpenLabServerFROG stands for FingeRprinting Ontology of Genomic variations. FROG fingerprints have been devised to capture genomic variations at various levels. Tools
ABiMSServerAnalysis and bioinformatics for Marine Science. Genomics
ABiMS-ToolsServerHosts tools/resources developed at the Station Biologique de Roscoff in collaboration with ABiMS. Tools
AGEseq @ AspenDBServerThis site provides a user-friendly interface for AGEseq (Analysis of Genome Editing by Sequencing) in a Galaxy instance. Tools
Alveo: Human Communication Science Virtual Laboratory ServerHuman Communication Science (HCS). Domain
ANASTASIAServerAutomated Nucleotide Aminoacid Sequences Translational plAtform for Systemic Interpretation and Analysis Genomics
Antigen Receptor Galaxy (ARGalaxy)ServerAutomate the analysis and visual reporting of T- and B-cell receptor repertoire sequencing data. Tools
APOSTLServerAutomated Processing of SAINT Templated Layouts (APOSTL) is a freely available software suite and analysis pipeline for reproducible, interactive analysis of AP-MS data. Tools
ARGs-OAPServerFast annotation and classification of antibiotic resistance gene-like sequences from metagenomic data. Tools
ARIESServerAnalysis 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-MAPServerLocally 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
BioBixServerA general genomics server. Includes the PROTEOFORMER pipeline tools. Genomics
BioCiphers Lab GalaxyServerBCL Galaxy gives a user friendly interface for analysis tools developed by the BioCiphers Lab at the University of Pennsylvania. Tools
BioMaSServerTaxonomic studies of environmental microbial communities Tools
BiominaServerA 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)ServerInsect genomics (aphids, parasitoïd wasps, lepidopterans) Domain
BitLABServerDetailed analysis of metagenomes. Tools
CBiB GalaxyServerA 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
Center for Phage Technology (CPT)ServerPhage biology and automated annotation. Domain
ChemFlowServerChemometrics without programming: infrared spectrometry on a Galaxy platform. Domain
Chemical Annotation Retrieval Toolkit (CART)ServerRetrieves annotations on biological effects of chemicals and determines which ones are enriched. Tools
ChimeRScopeServerFusion gene discovery from transcriptome-sequencing (RNA-seq) datasets. Tools
Cistrome Analysis PipelineServerChIP-chip/seq and gene expression data Domain
Codon HarmonizerServerEasily generate codon harmonized variants of gene sequences for heterologous expression Tools
CoSSciServerTools for solving Galton's problem in Comparative Research and complex network problems in Social Science. Domain
DBCLS GalaxyServerAdds text mining tools, DBCLS DBSearch Tools, semantic web tools Genomics
deepToolsServerdeepTools is a suite of user-friendly tools for the visualization, quality control and normalization of data from high-throughput DNA sequencing experiments. Tools
DintorServerGWA and NGS tools and modules for functional annotation of genes and gene products Domain
epiGeECServerCompare user-provided epigenomic datasets with thousands of public datasets. Tools
EpiToolKitServerComputational immunology for the development of novel epitope-based vaccines. Tools
Erasmus MCServerGeneral purpose genomics analysis, featuring many standard tools plus many additional tools. Genomics
GalaxEastServerIntegrative 'omics data analysis Genomics
Galaxy Integrated Omics (GIO)ServerProteomics Informed by Transcriptomics (PIT) methodology, and selection of surrogate peptides for targeted proteomics. Domain
Galaxy PGTB (Virtual Biodiversity Lab)ServerThis is a standard Galaxy instance implemented with specific tools for Biodiversity (Biodiversity Virtual Lab) and NGS (Ion Torrent from the PGTB facility) analysis. Domain
Galaxy TestServerBeta version of Galaxy Main Genomics
Galaxy-CEFAPServerGalaxy-CEFAP offers a set of tools to perform RNA-Seq and miRNA analysis. Domain
Galaxy-PServerGalaxy-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@GenOuestServerA general purpose Galaxy server Includes tools developped by Dyliss and GenScale bioinformatics research teams in Rennes, France. Genomics
Galaxy@PasteurServerGeneral purpose genomics analysis server. Genomics
Galaxy@PRABIServerIncludes 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
GeneLabServerNASA 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 HyperbrowserServerStatistical methodology and computing power to handle a variety of biological inquires on genomic datasets Domain
GigaGalaxyServerGigaGalaxy hosts tools and data analyses from papers published in *GigaScience*. Genomics
GrAPPAServerGrAPPA 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 BondingServerVisualize 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 GenomicsServerA simplified, workflow-centic interface to Galaxy, focused on genomics data from hardwood trees. Domain
Hunter College GalaxyServerA general purpose genomics server Genomics
Huttenhower LabServermetagenomic and functional genomic analyses, intended for research and academic use Domain
IBERS @ AberystwythServerSoftware, tools and pages written by IBERS researchers for release to the wider community. Tools
Image Analysis and Processing ToolkitServerImage analysis and processing. Domain
ImmPort GalaxyServerFlow Cytometry Analysis. Domain
In Silico GalaxyServerConstruction, analysis, and visualization of gene-gene interaction networks for sequencing data. Tools
Insitut CurieServerGeneral purpose genomic Galaxy server. Contains tools for Ion Torrent data, many RNA-Seq tools, ncPRO-seq, RSAT, Nebula tools, copy number and LOH tools, and NGS diagnostic tools. Genomics
International Rice Research Institute (IRRI) GalaxyServerBioinformatics workbench, with rice-specific data (i.e. genomes) and tools (mostly specialized for the IRRI Genotyping Service Laboratory) installed. Domain
IRProfilerServerImmune Repertoire Profiler (IRProfiler), a novel software pipeline that delivers a number of core receptor repertoire quantification and comparison functionalities on high-throughput TR and BcR sequencing data. Tools
kmer-SVMServerTool suite uses a support vector machine (SVM) with kmer sequence features to identify predictive combinations of short transcription factor binding sites which determine the tissue specificity of the original NGS assay. Tools
Koslicki LabServerWeb based access to tools created by the Koslicki Lab at Oregon State University. Tools
Langille LabServerPrediction of the unobserved character states in a community of organisms from phylogenetic information. Tools
LAPPS GridServerAn open, interoperable web service platform for natural language processing (NLP) research and development. Domain
LiSIsServerA platform for Virtual Screening. Tools
Majewski LabServerDetection of recurrent Allelic Imbalance in tumors using whole Exome sequencing data. Tools
Martin Luther U. Halle-WittenbergServerProvides implementations of InMoDe, CRISPRer, TALgetter, TALgetterLong, TALENoffer, and Dimont Tools
MBAC Metabiome PortalServerSimplifying control, usage, access, and analysis of microbiome, metabolome, and immunome data (the Metabiome). Tools
Metaproteomics GatewayServerMetaproteomics gateway providing access to documentation and other instructional materials, and an opportunity for hands-on training using example datasets and optimized metaproteomics workflows Domain
MGEScanServerIdentifying long terminal repeats (LTR) and non-LTR retroelements in eukaryotic genomic sequences. Tools
MiModD NacreousMapServerNacreousMap 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
MISSISSIPPIServerSupport 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)ServerA disease-specific open source web portal for Diabetes Mellitus. Domain
Molecular Property Diagnostic Suite - Tuberculosis (MPDSTB)ServerA disease-specific web portal for Tuberculosis for drug discovery and development. Domain
MPI-HLR Bioinformatics ServerServerHosts the MIRPIPE, ADMIRE, and LimiTT tools Tools
NebulaServerallows users (Bioinformaticians as far as Biologists) to analyze their ChIP-seq data. Domain
NELLYServerPlataforma de servicios para análisis de datos biomédicos en bioinformática featuring standard Galaxy Tools Genomics
NGS-QCServerEvaluate the quality of your favorite ChIP-seq or enrichment-related NGS dataset using NGS-QC Generator, which also includes a database with preprocessed profiles and a tutorial on how to analyze sequencing profiles yourself. Tools
OqtansServerCustomized Galaxy, extended with machine learning based tools for sequence and tiling array data analysis. Domain
OrioneServerA Galaxy based web server for microbiology. Orione includes all post mapping or assembling steps from scaffolding to complete annotation pipelines. Domain
OSDDlinux LiveGalaxyServerDrug discovery Domain
OsirisServerPhylogenetics Tools
PalfinderServerMicrosatellite development. Tools
PhenoMeNalServerLarge scale computing for medical informatics Domain
PIAServerPhylogenetics and gene interaction Tools
PIPE-CLIPServerReliable analysis of data generated by three types of CLIP-seq protocol: HITS-CLIP, PAR-CLIP and iCLIP. Tools
Pitagora-GalaxyServerThe Pitagora-Galaxy Project server intended for testing and sharing. Heavy analysis should be performed using the project's identical virtual machine (VM) or Amazon Machine Image (AMI). Genomics
PlantGenIEServerPlant Genome Integrative Explorer Galaxy instance Domain
PreSTIGEServerPredicting Specific Tissue Interactions of Genes and Enhancers Tools
Proteogenomics GatewayServerProvides 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
ProteoREServerProteoRE (Proteomics Research Environment) Domain
QBRC GalaxyServerHosts custom tools developed by members of the Quantitative Biomedical Research Center @ University of Texas Southwestern for statistical analysis of various High Throughput Sequencing experiments. Tools
RDF2GraphServerRDF2Graph recovers the structure of an RDF resource. Tools
RepeatExplorerServerGraph-based clustering and characterization of repetitive sequences, and detection of transposable element protein coding domains. Domain
RiboGalaxyServerTools for the analysis and visualization of ribo-seq data obtained with the ribosome profiling technique. Domain
RNA-Rocket @ Pathogen PortalServerSupports comparative analysis of host response to pathogens. It provides an RNA-Seq pipeline to characterize the transcriptome of all NIAID Bioinformatic Resource Center (BRC) pathogens and their key hosts. Domain
SIFTEDServerSpecificity Inference For TAL-Effector Design (SIFTED) Tools
South GreenServerGenomic resource analysis of southern and Mediterranean plants. Domain
SplicescopeServerPrediction of neuronal maturation using splicing profiles Tools
Stem Cell Discovery EngineServerDatabase of curated cancer stem cell experiments coupled to Galaxy. Domain
SymDServera platform for detecting internally symmetric protein structures Domain
UseGalaxy.euServerThe European UseGalaxy server. UseGalaxy
UseGalaxy.org (Main)ServerThe Galaxy Project free public server; biomedical research UseGalaxy
UseGalaxy.org.auServerThe Australian UseGalaxy server. UseGalaxy
USMI Galaxy DemonstratorServerThis Galaxy implementation is meant to demonstrate integration of microbial domain Biological Resource Center (mBRC) catalogues into the bioinformatics data integration environment. Tools
VarCapServerReliable prediction of different types of variants even at low frequencies. Tools
Vinther LabServerRNA structure-probing data analysis to improve the prediction of RNA secondary and tertiary structure and allow structural changes to be identified and investigated. Tools
VirAmpServerVirAmp is a web-based semi-de novo fast virus genome assembly pipeline designed for extremely high coverage NGS data. Domain
Wageningen URServerIncludes 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
Workflow4MetabolomicsServerA collaborative portal dedicated to metabolomics data processing, analysis and annotation. Domain
ZBIT Bioinformatics ToolboxServerThis customized version of the Galaxy webservice framework was set up to allow the public access of our bioinformatics tools. These tools were developed and implemented by members of the Department of Cognitive Systems at the University of Tübingen. 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.

ResourceLinkSummaryPurviewKeywords
CLIMBAcademicThe 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 KingdomGenomics
EGI MarketplaceAcademicGalaxy instances on a European wide federation of research cloud providers. GlobalGenomics
EuPathDB GalaxyAcademicA free, interactive, web-based platform for large-scale data analysis focused on eukaryotic pathogens. GlobalDomain
GenAPAcademicAll 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. CanadaGenomics
Globus GenomicsAcademicGlobus Genomics provides hardened high-performance Galaxy servers running with Globus on AWS. GlobalGenomics
JetstreamAcademicJetstream is part of XSEDE, a "collection of integrated advanced digital resources and services" and is funded by NSF. United StatesGenomics
Laniakea/INDIGO-DataCloudAcademicLaniakea 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. ItalyGenomics
MetaCentrumAcademicMetaCentrum 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. CzechiaGenomics
Nectar CloudAcademicSet up a Galaxy server on Australia's Nectar research cloud. AustraliaGenomics
NeLSAcademicLife Science platform for Norwegian academic researchers. NorwayGenomics
PL-GridAcademicThe PL-Grid project is free of charge for any Polish scientist. It is also free for any foreign collaborator of Polish scientists. PolandGenomics
SNIC Science Cloud (SSC)AcademicA national-scale cloud infrastructure for Swedish Academia SwedenGenomics
VectorBase GalaxyAcademicA full Galaxy server that includes reference information and workflows focusing on invertebrate vectors of human pathogens. GlobalDomain

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.

ResourceLinkSummaryKeywords
Amazon Web Services (AWS)CommercialSet up you own general purpose genomics server runing AWS using GVL and CloudMan. Genomics
MGEScanCommercialIdentifying long terminal repeats (LTR) and non-LTR retroelements in eukaryotic genomic sequences. Tools
OqtansCommercialCustomized Galaxy, extended with machine learning based tools for sequence and tiling array data analysis. Domain
Pitagora-GalaxyCommercialThe Pitagora-Galaxy Project server intended for testing and sharing. Heavy analysis should be performed using the project's identical virtual machine (VM) or Amazon Machine Image (AMI). Genomics

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.

ResourceLinkSummaryKeywords
ballaxyContainerHosts the BALL (Biochemical Algorithms Library) Project tools, i.e. computer aided drug design and molecular modelling based on protein and ligand structure data. Domain
CRAVAT-PContainerA Docker image containing a fully-operational Galaxy instance with pre-installed demonstration material for CRAVAT-P. Tools
deepToolsContainerdeepTools is a suite of user-friendly tools for the visualization, quality control and normalization of data from high-throughput DNA sequencing experiments. Tools
Galaxy basic sequence manipulationContainerGalaxy Docker repository for basic sequence data analysis. Domain
Galaxy BLAST+ContainerA complete and production ready Galaxy instance with installed BLAST+ tools. Domain
Galaxy ChIP-Seq DockerContainerGalaxy Docker image for ChipSeq analysis Domain
Galaxy CSGContainerGalaxy instance with tools for Constructive Solid Geometry shipped in a Docker container. Domain
Galaxy DockerContainerThe 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-SeqContainerGalaxy Docker repository for Exome sequencing data analysis Domain
Galaxy Genome AnnotationContainerGalaxy Docker repository for genome annotation Domain
Galaxy ImagingContainerGalaxy Docker repository for image analysis Domain
IRProfilerContainerImmune Repertoire Profiler (IRProfiler), a novel software pipeline that delivers a number of core receptor repertoire quantification and comparison functionalities on high-throughput TR and BcR sequencing data. Tools
RiboGalaxyContainerTools for the analysis and visualization of ribo-seq data obtained with the ribosome profiling technique. Domain
RNA WorkbenchContainermore 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
RNAcommenderContainerRNAcommender is a tool for genome-wide recommendation of RNA-protein interactions. It is a recommender system capable of suggesting RNA targets to unexplored RNA binding proteins, by propagating the available interaction information, taking into account the protein domain composition and the RNA predicted secondary structure. Tools
SMAGEXPContainerSMAGEXP (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
Workflow4MetabolomicsContainerA 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.

ResourceLinkSummaryKeywords
DDBJ Read Annotation PipelineVMAnnotates raw sequencing reads from next-generation sequencers(NGS) with high throughput, which are registered in DDBJ Read Archive (DRA). Tools
ImmunoGlobulin Galaxy (IGGalaxy)VMProvides a set of tools for easy detection and quantitation of immunoglobulin heavy chain alternative transcripts. Domain
KREAPVMKinetic Re-Epithelialization Analysis Pipeline Tools
Pitagora-GalaxyVMThe Pitagora-Galaxy Project server intended for testing and sharing. Heavy analysis should be performed using the project's identical virtual machine (VM) or Amazon Machine Image (AMI). Genomics



About This Directory

The Galaxy Project's public server usegalaxy.org can meet many needs, but it is not suitable for everything (see Choices for why). Fortunately the Galaxy Community has created Galaxy instances in many different forms and for many different applications.

This directory lists publicly accessible

  • Galaxy servers,
  • cloud services that support Galaxy instances, and
  • virtual machines and containers that can be easily deployed for your own server.

If you want to use Galaxy with little or no effort creating an instance, this is where you should start.

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. See the [UseGalaxy directory below](#usegalaxy-dir).

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.