Data Source Integration

An important goal of Galaxy is scalability. A major bottleneck when it comes to analysis of big data sets is the time and space it takes of copying these data sets.

Galaxy provides an interface such that it can communicate with other servers to get data directly into the Galaxy environment of a user without the need of “downloading” the data. In this hands on, we will use the resource from DoRiNA Server (Blin et al. 2014). but the main point about this short section is: if you have a data source which you think is very important for your research with Galaxy let us know!

Hands-on: Hands on!

1. Create a new history called “doRiNA”
2. Go to Get Data::doRiNA search
3. Choose hg19 from the drop-down list -> Search Database
4. Leave everything as is and choose from the Regulators (set A) drop-down list “hsa-let-7astar-CLASH” -> Search doRiNA
5. Use the “Send to Galaxy” button
6. Notice the new History Item

You can see the tutorial section of the DoRiNA website for more detailed examples. That was very easy for all of you! If you want your database of choice to be accessible as easy as this let us know!

Key points

• It is possible to couple an external data resource with a Galaxy server

• The external data resource is accessed through his native interface

• Data flows from the external data resource to the Galaxy server without the need of “downloading” the data

Frequently Asked Questions

References

1. Blin, K., C. Dieterich, R. Wurmus, N. Rajewsky, M. Landthaler et al., 2014 DoRiNA 2.0—upgrading the doRiNA database of RNA interactions in post-transcriptional regulation. Nucleic Acids Research 43: D160–D167. 10.1093/nar/gku1180

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Citing this Tutorial

1. Bérénice Batut, Saskia Hiltemann, Gianmauro Cuccuru, Helena Rasche, Data source integration (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/dev/tutorials/data-source-integration/tutorial.html Online; accessed TODAY
2. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
3. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{dev-data-source-integration,
author = "Bérénice Batut and Saskia Hiltemann and Gianmauro Cuccuru and Helena Rasche",
	title = "Data source integration (Galaxy Training Materials)",
	year = "",
	month = "",
	day = ""
	url = "\url{https://training.galaxyproject.org/training-material/topics/dev/tutorials/data-source-integration/tutorial.html}",
	note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
	doi = {10.1371/journal.pcbi.1010752},
	url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
	year = 2023,
	month = {jan},
	publisher = {Public Library of Science ({PLoS})},
	volume = {19},
	number = {1},
	pages = {e1010752},
	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
	editor = {Francis Ouellette},
	title = {Galaxy Training: A powerful framework for teaching!},
	journal = {PLoS Comput Biol} Computational Biology}
}

                   

Galaxy Administrators: Install the missing tools

You can use Ephemeris's shed-tools install command to install the tools used in this tutorial.

shed-tools install [-g GALAXY] [-a API_KEY] -t <(curl https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/data-source-integration/tutorial.json | jq .admin_install_yaml -r)

Alternatively you can copy and paste the following YAML

---
install_tool_dependencies: true
install_repository_dependencies: true
install_resolver_dependencies: true
tools: []

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