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Expand Up @@ -3,18 +3,18 @@ title: ENA data submission toolbox
contributors: [Bert Droesbeke, Flora D'Anna]
description: High scale publishing of data to ENA using easy to use metadata templates.
training:
- name: Screencast of the Galaxy ENA upload tool
- name: Submission of SARS-CoV-2 sequence data to ENA using Galaxy
registry: YouTube
url:
- name: Galaxy Training network
url: https://www.youtube.com/watch?v=POiQG-7O7rw
- name: "Galaxy Training network: Submitting sequence data to ENA"
registry:
url:
url: https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/upload-data-to-ena/tutorial.html
---


## Introduction

European Nucleotide Archive (ENA) is a fully open repository dedicated to storing raw sequencing data, assemblies, and annotation data. The ENA data submission toolbox simplifies the submission of sequence data, including raw reads and assembled sequences by offering a single-step submission process, a graphical user interface, tabular-formatted metadata and client-side validation, for every sample checklist supported at ENA.
[European Nucleotide Archive (ENA)](https://www.ebi.ac.uk/ena/browser/) is a fully open repository dedicated to storing raw sequencing data, assemblies, and annotation data. The ENA data submission toolbox simplifies the submission of sequence data, including raw reads and assembled sequences by offering a single-step submission process, a graphical user interface, tabular-formatted metadata and client-side validation, for every sample checklist supported at ENA.


## Its components
Expand All @@ -27,52 +27,56 @@ European Nucleotide Archive (ENA) is a fully open repository dedicated to storin
Command line tool allowing submission of raw reads data and respective metadata to ENA using tabular files or an excel sheet. Programmatically submit study, sample, run and experiment objects without the need of logging in to the ENA Webin interface.

Key features:
- Submission of raw reads data and metadata
- Using tabular files or an excel sheet to easily capture the metadata
- Add, modify, cancel and release study, experiment, run and sample objects
- Submit raw sequencing data and metadata
- High volume submissions
- Support for all sample types
- Use tabular files or an excel sheet to easily capture the metadata
- Add, modify, cancel and release study, experiment, run and sample objects taking away the need
- Safe credential management using a credentials file
- Client side validation using ENA checklists (samples) and official ENA XSD files (run, experiment and study)
- Can the provided tsv/xlsx templates to fill in the metadata
- Compatible with the provided tsv/xlsx templates to fill in the metadata (see below)

[<i class="fa-brands fa-github me-2"></i>Github](https://github.com/usegalaxy-eu/ena-upload-cli){: class="btn btn-primary rounded-pill"}
[<i class="fa-solid fa-download me-2"></i>Install using pip](https://pypi.org/project/ena-upload-cli/){: class="btn btn-primary rounded-pill"}
[<i class="fa-brands fa-github me-2"></i>Documentation + source](https://github.com/usegalaxy-eu/ena-upload-cli){: class="btn btn-light border rounded-pill"}
[<i class="fa-solid fa-download me-2"></i>Install using pip](https://pypi.org/project/ena-upload-cli/){: class="btn btn-light border rounded-pill"}

### Galaxy

[Galaxy](https://galaxyproject.org/eu/) is an open-source platform for FAIR data analysis that enables users to use tools from various domains through its graphical web interface.
Following tool wrappers make Galaxy your one stop shop for data preprocessing, analysing and submitting. Both tools can be installed through the Galaxy toolshed. Ask the administrator of you Galaxy instance if this is not yet the case.
[Galaxy](https://galaxyproject.org/eu/) is an open-source platform for FAIR data analysis that enables users to use tools from various domains through its graphical web interface.Following tool wrappers make Galaxy your one stop shop for data preprocessing, analysing and submitting. Both tools can be installed through the Galaxy toolshed. Ask the administrator of you Galaxy instance if this is not yet the case.

#### Galaxy ENA upload tool

Galaxy tool wrapper of the ENA-upload-cli. Gives the command line tool a graphic user interface and adds support for interactive submissions.
This isn the Galaxy tool wrapper of the ENA-upload-cli mentioned above. The integration with Galaxy gives the command line tool a graphic user interface and adds support for interactive submissions.

Key features:
- Graphical user interface making it easy to use
- Raw read submissions
- ENA-upload-cli wrapper
- ENA-upload-cli at its core
- Add and modify ENA objects
- User based credential management
- Possibility to set a brokering account
- Possibility to set a system-wide brokering account
- Easy data upload/management
- Available @ useGalaxy.eu, .be and .au

[<i class="fa-solid fa-play me-2"></i>Use at useGalaxy.be](https://usegalaxy.be/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fena_upload%2Fena_upload){: class="btn btn-primary rounded-pill"}
[<i class="fa-brands fa-github me-2"></i>Github](https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload){: class="btn btn-primary rounded-pill"}
- Available at [useGalaxy Europe](https://usegalaxy.eu/), [useGalaxy Belgium](https://usegalaxy.be/) and [useGalaxy Australia](https://usegalaxy.org.au/)

[<i class="fa-solid fa-play me-2"></i>Use at useGalaxy.be](https://usegalaxy.be/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fena_upload%2Fena_upload){: class="btn btn-light border rounded-pill"}
[<i class="fa-brands fa-github me-2"></i>Source](https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload){: class="btn btn-light border rounded-pill"}
[<i class="fa-solid fa-graduation-cap me-2"></i>Tutorial on GTN](https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/upload-data-to-ena/tutorial.html#submitting-raw-sequence-data-reads-to-the-ena){: class="btn btn-light border rounded-pill"}
[<i class="fa-solid fa-download me-2"></i>Galaxy toolshed](https://toolshed.g2.bx.psu.edu/repository?repository_id=0db04aa13ef9d2f8){: class="btn btn-light border rounded-pill"}


#### Galaxy assembly submission tool

Galaxy wrapper to submit consensus sequences to ENA in an interactive way. The tool has the [Webin-CLI](https://github.com/enasequence/webin-cli) script of ENA as core and supports all sample checklists.
Galaxy wrapper to submit consensus sequences to ENA in an interactive way. The tool has the [Webin-CLI](https://github.com/enasequence/webin-cli) script of ENA at its core and supports all sample checklists.

Key features:
- Interactive submission of the metadata
- Possibility to set a brokering account
- Easy data upload/management
- Available @ useGalaxy.be
- Available at [useGalaxy Belgium](https://usegalaxy.be/)

[<i class="fa-solid fa-play me-2"></i>Use at useGalaxy.be](https://usegalaxy.be/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fieguinoa%2Fena_webin_cli%2Fena_consensus_submit){: class="btn btn-primary rounded-pill"}
[<i class="fa-brands fa-github me-2"></i>Github](https://github.com/usegalaxy-be/galaxytools/tree/main/consensus_sequence_ena_galaxy){: class="btn btn-primary rounded-pill"}
[<i class="fa-solid fa-play me-2"></i>Use at useGalaxy.be](https://usegalaxy.be/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fieguinoa%2Fena_webin_cli%2Fena_consensus_submit){: class="btn btn-light border rounded-pill"}
[<i class="fa-brands fa-github me-2"></i>Source](https://github.com/usegalaxy-be/galaxytools/tree/main/consensus_sequence_ena_galaxy){: class="btn btn-light border rounded-pill"}
[<i class="fa-solid fa-graduation-cap me-2"></i>Tutorial on GTN](https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/upload-data-to-ena/tutorial.html#submitting-consensus-sequences-to-ena){: class="btn btn-light border rounded-pill"}
[<i class="fa-solid fa-download me-2"></i>Galaxy toolshed](https://toolshed.g2.bx.psu.edu/repository?repository_id=dfa4f0fc31027b52){: class="btn btn-light border rounded-pill"}


### Metadata templates
Expand All @@ -81,26 +85,27 @@ Tabular-format and xlsx spreadsheet metadata templates required to submit data t

Key features:
- GitHub repo hosting tsv and xlsx templates for every checklist
- GitHub Actions to keep up to date with ENA XSD/checklist files
- GitHub Actions to keep up to date with ENA XSD/checklist files to guarantee compatibility
- Versions in sync with the ones from ENA-upload-CLI

[<i class="fa-brands fa-github me-2"></i>Github](https://github.com/ELIXIR-Belgium/ENA-metadata-templates){: class="btn btn-primary rounded-pill"}
[<i class="fa-brands fa-github me-2"></i>Documentation + source](https://github.com/ELIXIR-Belgium/ENA-metadata-templates){: class="btn btn-light border rounded-pill"}

### Docker deployment

When you can not use the Galaxy instances @ useGalaxy.eu, .be and .au, possibly due to GDPR reasons, we also offer ready to use Docker containers. The Docker container is shipped with the previously mentioned Galaxy tools and deploys locally a fully usable Galaxy instance.
When you can not use the Galaxy instances at useGalaxy.eu, .be and .au, possibly due to GDPR reasons, we also offer a ready to use Docker container. The Docker container is shipped with the previously mentioned Galaxy tools and deploys locally a fully usable Galaxy instance.

Key features:
- Easy deployment of a local Galaxy instance
- Developed during COVID-19
- Data stays on-premise until submission
- The Galaxy instance contains:
- Tool to easily clean raw reads from human reads
- Contains:
- ENA-upload tool
- ENA Assembly submission tool
- Tool to easily clean raw reads from human reads
- Workflows to perform SARS-CoV-2 analysis

[<i class="fa-brands fa-github me-2"></i>Github](https://github.com/ELIXIR-Belgium/ena-upload-container){: class="btn btn-primary rounded-pill"}
[<i class="fa-brands fa-github me-2"></i>Documentation + source](https://github.com/ELIXIR-Belgium/ena-upload-container){: class="btn btn-light border rounded-pill"}
[<i class="fa-solid fa-download me-2"></i>Download image from Quay.io](https://quay.io/repository/galaxy/ena-upload){: class="btn btn-light border rounded-pill"}


## Using DataHub to manage your metadata

Expand All @@ -115,9 +120,10 @@ Key features:
- Existing ISA-JSON export function
- ISA-JSON as machine actionable metadata carrier

[<i class="fa-solid fa-play me-2"></i>Try out on DataHub](https://datahub-test.elixir-belgium.org/){: class="btn btn-primary rounded-pill"}
[<i class="fa-solid fa-play me-2"></i>Try out on DataHub](https://datahub-test.elixir-belgium.org/){: class="btn btn-light border rounded-pill"}


## Publication

Roncoroni, M., Droesbeke, B., Eguinoa, I., De Ruyck, K., D’Anna, F., Yusuf, D., Grüning, B., Backofen, R., & Coppens, F. (2021). A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive. Bioinformatics, 37(21), 3983–3985. [https://doi.org/10.1093/bioinformatics/btab421](https://doi.org/10.1093/bioinformatics/btab421)

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