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ReGaTE: Registration of Galaxy Tools in Elixir.
Olivia Doppelt-Azeroual1, Fabien Mareuil1, Eric Deveaud1
1Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 Institut Pasteur et CNRS), 25 rue du Docteur Roux, Paris, France.
Gigascience
|April 13, 2017
Summary
ReGaTE automates the registration of Galaxy tools in the ELIXIR registry (bio.tools). This enhances bioinformatics tool discovery and accessibility for researchers worldwide.
Area of Science:
- Bioinformatics
- Computational Biology
- Software Engineering
Background:
- Bioinformaticians rely on diverse software tools and data sources.
- Existing cataloguing initiatives guide tool selection.
- The ELIXIR Tools and Data Services Registry (bio.tools) serves as a central information hub.
- Workflow environments like Galaxy accelerate bioinformatics experiment design and automation.
Purpose of the Study:
- To develop an automated solution for registering Galaxy services in bio.tools.
- To address the lack of a convenient mechanism for mass registration of Galaxy instances.
- To enhance the discoverability of bioinformatics tools and services.
Main Methods:
- Introduction of ReGaTE (Registration of Galaxy Tools in Elixir) software utility.
- Utilizing the BioBlend application program interface to extract metadata from Galaxy servers.
- Enhancing extracted metadata with scientific information required by bio.tools.
- Automated pushing of service metadata to the bio.tools registry.
Main Results:
- ReGaTE enables fast and convenient publication of Galaxy services in bio.tools.
- Increased visibility for registered Galaxy services.
- Enrichment of the bio.tools software discovery function.
- Freely available source code on Github.
Conclusions:
- ReGaTE streamlines the process of making Galaxy services accessible through bio.tools.
- Facilitates wider adoption and utilization of bioinformatics tools within the research community.
- Promotes reproducibility and efficiency in bioinformatics workflows.