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ReGaTE, Registration of Galaxy Tools in Elixir

ReGaTE, Registration of Galaxy Tools in Elixir. Olivia Doppelt-Azeroual, Fabien Mareuil, Eric Deveaud, Matus Kalas, and Hervé Menager. 07/07/2015. Plan. INTRODUCTION. PART 2. Original questions. ReGaTE. CONCLUSION. PART 1. Elixir Registry. & Perspectives. INTRODUCTION.

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ReGaTE, Registration of Galaxy Tools in Elixir

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  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

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