Galaxy France: an example of a national UseGalaxy server
Creators: name: Cléa Siguret
name: Chaussepied, Thomas
name: Libouban, Romane
name: Mercier, Eva
name: Seiler, Julien
name: Batut, Bérénice
name: Corguillé, Gildas Le
name: Bretaudeau, Anthony
Publisher: name: F1000 Research Limited
Year: 2024

description: Created in 2021, UseGalaxy France (UseGalaxy.fr) is the first national UseGalaxy server. It is the French national instance hosted by the <b>French Institute for Bioinformatics</b> (IFB - ELIXIR-FR) <b>Core Cluster </b>(8300 CPU-cores, 52 TB of RAM, GPU cards) and maintained by IFB itself and by engineers from regional platforms. It offers <b>3k+ tools and several Interactive tools (GxIT) like Jupyter Notebook, AlphaFold, and Helixer. Since 2021, its 6k+ users ran 3.6M+ jobs.</b><br>
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UseGalaxy.fr is well embedded within the French ecosystem. UseGalaxy.fr is involved in many <b>national projects</b> (e.g. ABRomics, the national platform for antimicrobial resistance surveillance) but also European efforts such as <b>EuroScienceGateway</b>. It hosts several community-specific <b>subdomains</b>: ecology, metabarcoding, proteore, covid19, workflow4metabolomics, MNHN, and Plants-pathogens. New subdomains are currently being integrated into UseGalaxy.fr. <br>
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Several local servers (e.g. ABIMS, GenOuest/BIPAA, IGBMC) have decided to <b>migrate</b> to UseGalaxy.fr over the last few years. Other local servers from the French Galaxy Working Group have mentioned their interest in following the same pathway. <br>
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Since the first day, UseGalaxy.fr has followed the wake of the UseGalaxy servers. It’s implemented as an Infrastructure as Code (<b>IaC</b>) infrastructure, stored on GitLab, managed by Ansible, and launched by GitLab-runner. The whole system is co-administered by a team of 6 IFB members from multiple regional platforms.<br>
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The developments of UseGalaxy.fr are focused on the adoption of best practices for the deployment of UseGalaxy servers, in particular as one of the 7 national servers supported by the EuroScienceGateway project. As such, tools are installed using a standard GitLab repository and auto-updated by a bot (IFBOT) once a week. Tool dependencies are currently managed using Conda, but are progressively moving to be fully based on Apptainer. Data managers are automatically installed but are still manually launched, though this limitation should be solved by the planned adoption of IDC (Simon's Data Club) mechanism. Recently UseGalaxy.fr was configured to use the new Total Perspective Vortex (TPV), using community but also local rules to dynamically assign tool resources.<br>
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As part of the <b>EuroScienceGateway</b> project, UseGalaxy.fr aims to integrate a European Pulsar network, allowing the execution of jobs from other UseGalaxy servers on the IFB infrastructure, but also the submission of UseGalaxy.fr jobs on other computing infrastructure, in France and abroad. A first French Pulsar node is already hosted on the GenOuest regional platform.<br>
UseGalaxy.fr also provides a Training Infrastructure as a Service (<b>TIaaS</b>). Since February 2022, this service has offered 550+ days of computing to 70+ events, reaching 1700+ learners.<br>
All support on UseGalaxy.fr is done as a community effort, using the public Discourse hosted by IFB (https://community.france-bioinformatique.fr/).<br>
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In this talk, we will present the UseGalaxy France server, a first successful implementation of a national UseGalaxy server, and share our plans for the future, in particular for better integration with the other UseGalaxy servers.