REPORT: Workbench integration enabler: implementation & evaluation of impact

The objective of EXCELERATE Deliverable 1.6 is to integrate the ELIXIR Tools and Data Services Registry (bio.tools) with workbench environments such as Galaxy, respecting the general trend towards the use of workflows as a preferred environment for the convenient use of tools and data access, especially when resources must be used in combination with one another. The ELIXIR EXCELERATE proposal envisioned integration in two ways: 
A Workbench Integration Enabler service to develop the vision “register your software once - enable its support everywhere”. The idea, technically, is to translate the description of any tool or service that is registered in bio.tools, into the metadata format required by the existing major workbench environments. In so, doing, the cost ofmaintaining quality tool description for us in workbench environments is lowered, giving a practical boost to tool interoperability.
A utility for en masse registration of services from Galaxy instances. In the context of a generic registry for bioinformatics software, such as bio.tools, Galaxy instances constitute a major source of valuable content (online services and underlying tools). The idea is to provide a sustainable means to harvest this content.

We have made major strides in delivering this functionality, having published two papers with a third in preparation:
Ménager, H., Kalaš, M., Rapacki, K. and Ison, J. (2016). Using registries to integrate bioinformatics tools and services into workbench environments. Int J Softw Tools Technol Transfer, doi:10.1007/s10009-015-0392-z Hillion KH, Ison J and Ménager H. (2017). ToolDog – generating tool descriptors from the ELIXIR tool registry. [version 1; not peer reviewed]. F1000Research 2017, 6:767

(poster). doi:10.7490/f1000research.1114125.1
Doppelt-Azeroual, O., Mareuil, F., Deveaud, Kalaš, M., Soranzo, N., van den Beek, M.,
Grüning, B., Ison, J. and Ménager, H. (2017). ReGaTE: Registration of Galaxy Tools in Elixir. GigaScience, doi:10.1093/gigascience/gix022

The first article (Ménager et al.) outlines the general strategy behind the Workbench Integration Enabler service, scopes the problem, and provides the technical groundwork. The second (Hillion KH et al.) is a poster summarising progress thus far in implementing this service and the basis for a publication in preparation. The third (Doppelt-Azeroual et al.) describes a utility for en masse registration of services from Galaxy instances, which has been applied to the registration of services from the Galaxy instance hosted by Institut Pasteur, as described in D1.2 report.

For this deliverable report, we attach and summarise the publications in press. The software is available under open source license:

ToolDog (MIT license) https://github.com/bio-tools/ToolDog
ReGaTE (GPL license) https://github.com/C3BI-pasteur-fr/ReGaTE