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Welcome to the nomad-eosc-galaxy-actions documentation

A NOMAD Actions plugin for the EOSC demonstrator with Galaxy.

What this plugin does

NOMAD is FAIRmat's research data platform for Materials Science; Galaxy is a widely-used scientific workflow platform. This NOMAD plugin connects the two: it provides NOMAD Actions (NOMAD's plugin entry point for long-standing asynchronous tasks) — that take data already stored in NOMAD, sends them to Galaxy to run tools abd workflows, and links the annotated result back into NOMAD as a new entry once the Galaxy run completes.

Currently, one Action is implemented: find_peaks, which sends an XPS spectrum to a Galaxy workflow bundling its XPS peak finding tool (built on pynxtools-xps) for peak detection. The interface itself is generic, so this is meant to be the first of several Actions, not the only one.

The round trip end to end:

Entry in NOMAD --> Action trigger --> NOMAD Action --> Galaxy workflow run
                                                            │
New NOMAD entry <-------------------------------------------┘

This is an interoperability demonstrator in the context of the German node of the European Open Science Cloud (EOSC). It cuts both ways: for NOMAD, the concrete goal is to show that a NOMAD-stored dataset can be processed by an external workflow platform like Galaxy without leaving NOMAD's data model, and that the round trip is reproducible and inspectable on both sides; for Galaxy, it shows that Galaxy can interface with other platforms under the EOSC node, with NOMAD as an example. See the Explanation page for the full technical picture, including the contract this plugin relies on from the Galaxy side.

Introduction

Tutorial

New to this plugin? Or are you from the Galaxy team and want to see the round trip work without a NOMAD deployment? Start here.

How-to guides

How-to guides provide step-by-step instructions for a wide range of tasks, with the overarching topics:

Explanation

The Explanation section provides background knowledge on this plugin.

Reference

The Reference section includes all CLI commands and arguments, all configuration options, the possible schema annotations and their arguments, and a glossary of used terms.

Contact

For questions or suggestions:

Project and community

The work is funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - 460197019 (FAIRmat).