ReGaTE: Registration of Galaxy Tools in Elixir

Abstract

Background: Bioinformaticians routinely use multiple software tools and data sources in their day-to-day work and have been guided in their choices by a number of cataloguing initiatives. The ELIXIR Tools and Data Services Registry (bio.tools) aims to provide a central information point, independent of any specific scientific scope within bioinformatics or technological implementation. Meanwhile, efforts to integrate bioinformatics software in workbench and workflow environments have accelerated to enable the design, automation, and reproducibility of bioinformatics experiments. One such popular environment is the Galaxy framework, with currently more than 80 publicly available Galaxy servers around the world. In the context of a generic registry for bioinformatics software, such as bio.tools, Galaxy instances constitute a major source of valuable content. Yet there has been, to date, no convenient mechanism to register such services en masse. Findings: We present ReGaTE (Registration of Galaxy Tools in Elixir), a software utility that automates the process of registering the services available in a Galaxy instance. This utility uses the BioBlend application program interface to extract service metadata from a Galaxy server, enhance the metadata with the scientific information required by bio.tools, and push it to the registry. Conclusions: ReGaTE provides a fast and convenient way to publish Galaxy services in bio.tools. By doing so, service providers may increase the visibility of their services while enriching the software discovery function that bio.tools provides for its users. The source code of ReGaTE is freely available on Github at https://github.com/C3BI-pasteur-fr/ReGaTE.

BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows

“…EDAM annotations allow to classify tools according the type of data they consume or produce and provides a controlled vocabulary to define their precise functionality. This information has been used to derive tools’ annotation for CWL, or Galaxy 44,45 automatically. Unfortunately, ontology terms for structural bioinformatics, in general, and biomolecular simulation specifically, were scarce in EDAM.…”

An architecture for genomics analysis in a clinical setting using Galaxy and Docker

“…The Dockerized Galaxy embedding examples of Dockerized tools (Docker in Docker), the ReGaTE [ 37 ] traceability metadata creation system, configuration files, and code, and the AnalysisManager module (see Fig. 3 ) connecting a sequencer to the services of the Galaxy platform directly can be found online [ 38 ].…”

“…A metadata file is generated along with the result detailing the input parameters and the version of the tool. We leverage the ReGaTE metadata system [ 37 ], which itself uses EDAM [ 44 ] ontology for bioinformatics processes. Reproducibility.…”

“…ReGaTE [ 37 ] aims at automating the publication of Galaxy tools in the ELIXIR bio-tools registry by generating EDAM ontologies annotations [ 29 ]. The EDAM ontology goal is to describe and characterize bioinformatics operations such as data types and format.…”

Using bio.tools to generate and annotate workbench tool descriptions

“…A significant part of the metadata stored in the descriptions is, however, common to registries and workbench environments systems 19 , and strategies relying on a mapping between these different description formats can help avoid redundancy and mislabeling of tools Figure 1 ). The ReGaTE utility 20 illustrates this by using tool descriptions from Galaxy to publish available services on bio.tools. Another application is to facilitate workbench environment integration, by reusing tool descriptions from registries.…”