Tool assembly: Galaxy
What is Galaxy?
Galaxy is a well-known open-source platform for FAIR data analysis that enables users to:
- access and collect data from reference databases, external repositories and other data sources;
- use tools from various domains that can be plugged into workflows through its graphical web interface;
- run code in interactive environments (RStudio, Jupyter…) along with other tools or workflows;
- manage data by sharing and publishing results, workflows, and visualizations;
- capture the metadata of data analyses, thus ensuring their reproducibility.
Galaxy supports scientists to perform accessible, reproducible, and transparent computational analysis. The Galaxy Community is actively involved in helping the ecosystem improve and sharing scientific discoveries.
Who can use Galaxy?
Galaxy also provides open infrastructure ready to use for researchers worldwide. All what you need is a web browser and an account in a public server:
What can you use Galaxy for?
Galaxy can be used at different stages of the data life cycle, covering from the data collection to the reuse steps.
Collect
Access to databases
- UniProt
- InterMine
- OMERO
- OmicsDI
- Copernicus
- UCSC genome browser (tutorial)
- NCBI datasets
- INSDC (ENA)
- PDB
- 3rd-party databases
Customised data access
- Data libraries
- BYOD (Posix, WebDav, Dropbox, ...)
- On-demand reference data
- Deferred data from remote locations
LIMS integration
- Connect to sequencing facilities
- Rich API for integration with LIMS
Process
Data transformation
- Data transformation tools
- Quality control
- Data cleaning
- Annotation
- Interactive Tools (OpenRefine, RStudio, Jupyter Notebook)
Import workflows
Metadata handling
- Provenance tracking
- Automatic metadata enrichment
- Bulk (meta)data manipulation
Analyse
Preserve
Export artefacts
- Workflows
- History
- Datasets
Formats
- Archive file
- BioCompute Object
- RO-Crate (WIP)
Export to remote sources
- FTP
- Dropbox
- S3 Bucket
- AWS
- GDrive
- Nextcloud
- WebDav
- Google Cloud Storage
Share
Share artefacts
- Datasets
- Histories
- Workflows
- Visualizations
- GA4GH Beacon (WIP)
- DRS server
Shareability
- RBAC (Role-Based Access Control)
- One user
- A group of users
- Public
Reuse
Account cleaning
- Storage dashboard to manage quota
- Bulk (permanent) delete
- Quota temporarily extendable
- Multiple quota per object storage (WIP)
Import artefacts
- Histories (own, shared by others)
- Workflows from the WorkflowHub
Related pages
Your tasks
Data analysis
How to make data analysis FAIR. Data organisation
Best practices to name and organise research data. Data publication
How to prepare data and find repositories for publication. Data quality
How to ensure high quality of research data. Existing data
How to find and reuse existing data. Identifiers
How to use identifiers for research data. Machine actionability
How to make machine-actionable (meta)data. Documentation and metadata
How to document and describe your data.
How to make data analysis FAIR. Data organisation
Best practices to name and organise research data. Data publication
How to prepare data and find repositories for publication. Data quality
How to ensure high quality of research data. Existing data
How to find and reuse existing data. Identifiers
How to use identifiers for research data. Machine actionability
How to make machine-actionable (meta)data. Documentation and metadata
How to document and describe your data.
More information
Relevant tools and resources
Skip tool table| Tool or resource | Description | Related pages | Registry |
|---|---|---|---|
| Galaxy | Open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses. | NeLS Marine Metagenomics Data analysis Researcher Data Steward: infrastructure IFB | Tool info Training |
Amandine Nunes-Jorge
Beatriz Serrano-Solano