1 / 15

ReGaTE, Registration of Galaxy Tools in Elixir

Explore the implementation of ReGaTE, a tool facilitating the registration of Galaxy tools in Elixir for bioinformatics analysis. Learn about its history, challenges, installation process, and future perspectives. Enhance your understanding of how to efficiently manage bioinformatics tools and data services with ReGaTE.

capehart
Download Presentation

ReGaTE, Registration of Galaxy Tools in Elixir

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. ReGaTE, Registration of Galaxy Tools in Elixir Olivia Doppelt-Azeroual, Fabien Mareuil, Eric Deveaud, Matus Kalas, and Hervé Menager 07/07/2015

  2. Plan INTRODUCTION PART 2 Original questions ReGaTE CONCLUSION PART 1 Elixir Registry & Perspectives 2/16  Olivia Doppelt-Azeroual • ReGaTE  07/07/2015

  3. INTRODUCTION Original questions 3/16  Olivia Doppelt-Azeroual • ReGaTE  07/07/2015

  4. (A regate is a boat race in French) 1.1 Original Questions RNAseq metagenomic ? proteomics Agent detection fastQ BAM VCF On what kind of project does he work ? What kind of data does he have/want ? Krona report fasta Data analyst A Galaxy instance A cluster with admins What ressources does he have access to ? Not much A virtual machine 4/16  Olivia Doppelt-Azeroual • ReGaTE  07/07/2015

  5. 1.2 Start answering, with a galaxyst ? • if using a Galaxy with admin knowledge  Search in a Toolshed and build analysis workflows but … WARNING !! HOW ARE TOOLS CLASSIFIED ? NOT ALL TOOLS ARE IN GALAXY 5/16  Olivia Doppelt-Azeroual • ReGaTE  07/07/2015

  6. PART 1 Elixir Registry 6/16  Olivia Doppelt-Azeroual • ReGaTE  07/07/2015

  7. 2.1 ELIXIR Tools and Data Services Registry • Why A registry? • A registry addresses the question of resource discovery • Aims in FINDING and UNDERSTANDING relevant resources by various means • Gives relevant information on that resource • Tells how to access it (web services’ url, download pages, …) • Why THIS registry? • Uses EDAM ontology: a CONTROLLED vocabulary to define bioinformatics tools operation, topics, datatypes and data formats. • Coupled with workbenchs like Mobyle, Galaxy, … who have become, very useful resources providers, • Enabling a decentralized registry, maintained by the resource specialist themselves TOOL VISIBILITY !! 7/16  Olivia Doppelt-Azeroual • ReGaTE  07/07/2015

  8. PART 2 ReGaTE 8/16  Olivia Doppelt-Azeroual • ReGaTE  07/07/2015

  9. 3.1ReGaTE: History facts • In June 2014: • The toolinfowarehouse subproject was initiated during an EDAM meeting. •  AIM: key resource providers to gather data about bioinformatics tools • The IDEA: •  Use them to start filling “massively” the ELIXIR Registry • ReGaTE, stands for Registration of Galaxy Tools in Elixir: • Uses Bioblend API to extract information concerning installed tools on any Galaxy; tools.show_tool (io_details=True) to get input/output information • Resulting JSON structure files for each installed tool Pasteur cluster tools Import script EDAM ontology Mobyle Import script tool.json Tool registry format Galaxy Import script Tool registry interface Debian-med Import script 9/16  Olivia Doppelt-Azeroual • ReGaTE  07/07/2015

  10. 3.2ReGaTE: Challenges • The dictionary returned by the Bioblend show_tool function can be as complex as the Galaxy xml itself • Galaxy datatypes are a challenge by themselves  • The function field is a key field in Elixir Registry (ER), it gathers: • functionName, functionDescription, functionHandle, input [dataFormat, dataType], output [dataFormat, dataType]  the red fields are EDAM based Adding extensions to show_tool fork to add edam_format to /lib/galaxy/datatypes + gist mapping : in EDAM 1.11 EDAM mapping in datatypes_conf.xml GCC Oct Jun Mar May 2014 2015 Contact GT New types for EDAM are defined [yaml file for datatypes/EDAM mapping] + [Regate/json with EDAM terms updated in ER] + BioBlend fork + DOC Regate with extensions + inserted in ER 10/16  Olivia Doppelt-Azeroual • ReGaTE  07/07/2015

  11. 3.3ReGaTE: How it works… ##Installation process: #pip install –e git+https://github.com/bioinfo-center-pasteur-fr/ReGaTE.git#egg=regate #pip install –r src/regate/requirements.txt EDAM edam mapping yaml json remag.py regate.py Import2er.py 11/16  Olivia Doppelt-Azeroual • ReGaTE  07/07/2015

  12. CONCLUSION & Perspectives 12/16  Olivia Doppelt-Azeroual • ReGaTE  07/07/2015

  13. To resume… • Some of our jsons are in the registry, key words: “galaxy institut pasteur” • If interested to display your Galaxy tools in the ER •  Use ReGaTE to generate the json files, we tested on severalGalaxy servers • You only need a galaxy updated after Oct 2014, an activated API and an API key to enable the use of BIOBLEND • To insert the JSONs in the Registry, you need to contact the registry group using the mailing list registry@elixir-dk.org. 13/16  Olivia Doppelt-Azeroual • ReGaTE  07/07/2015

  14. Conclusion & Perpectives • The ReGaTE tool is the result of a highly productive collaboration between CBS in Denmark, University of Bergen in Norway, The Institut Pasteur in Paris and the Galaxy Team. • It is on GiHub: https://github.com/bioinfo-center-pasteur-fr/ReGaTE, with a first version documentation. • The addition of EDAM in Galaxy will simplify datatypes management. • Nice to interact with the Galaxy Team. • To finish, I’d say that EDAM for galaxy datatypes in only a first step. Indeed, with the French Galaxy workgroup we are planning to work on an “edamization” of the toolshed. (EDAM Operations and Topics to annotate tools) 14/16  Olivia Doppelt-Azeroual • ReGaTE  07/07/2015

  15. THANK YOU ! 15/16  Olivia Doppelt-Azeroual • ReGaTE  07/07/2015

More Related