# Galaxy France: an example of a national UseGalaxy server

Clea Siguret, Thomas Chaussepied, Romane Libouban, Eva Mercier, Julien Seiler, Bérénice Batut, Gildas Le Corguillé, Anthony Bretaud

► To cite this version:

Clea Siguret, Thomas Chaussepied, Romane Libouban, Eva Mercier, Julien Seiler, et al. Galaxy France: an example of a national UseGalaxy server. GCC 2024 - Galaxy Community Conference, Jun 2024, Brno, Czech Republic. pp.1-15, 10.7490/f1000research.1119767.1 . hal-04644627

HAL Id: hal-04644627

https://hal.science/hal-04644627v1

Submitted on 11 Jul 2024

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Distributed under a Creative Commons Attribution 4.0 International License
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An example of a national
UseGalaxy server

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# The French Institute of Bioinformatics - IFB / ELIXIR-FR

## Services, training, innovative developments for life sciences

## A distributed national infrastructure

**IFB Core Cluster: a national HPC infrastructure for life science**

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Currently

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97 nodes

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8396 cpu
threads

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52 To RAM

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4 Po storage

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6 GPU cards
NVIDIA A100
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The French **Galaxy Working Group** v1.0 - 2016-2019
Network of small scale server admins

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Galaxy
wg

Objectives:

1. Meeting every 2 months

2. Connect Galaxy users, developers, admins across France

3. Share knowledge

4. Training

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IFB

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INSTITUT FRANÇAIS DE BIINFORMATIQUE
1. Many small scale Galaxy instances

2. Many Galaxy administrators struggling

3. Some projects needing visibility

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1. Many small scale Galaxy instances

2. Many Galaxy administrators struggling

3. Some projects needing visibility

One solution - One instance - One admin group

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Galaxy
FRANCE

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1. Many small scale Galaxy instances

2. Many Galaxy administrators struggling

3. Some projects needing visibility

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Galaxy

EUROPE

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1. Many small scale Galaxy instances

2. Many Galaxy administrators struggling

3. Some projects needing visibility

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One solution - One instance - One admin group

So do we need a national server?

⇒ YES!

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Galaxy
EUROPE

Galaxy
FRANCE

1. French bread and a croissant

Support FR community

2. We already have the HPC resources (IFB)

3. Take our part of the load

4. Sovereignty / independence

5. “Proximity” aspects: treat data locally

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IFB

INSTITUT FRANÇAIS DE BIINFORMATIQUE

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## UseGalaxy.fr

Launch: 2019

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6.5k Users

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4.5M Jobs

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3k Active
Users

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1.5M+ Jobs

Host: Institut Français de Bioinformatique

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1.7k+ Tools

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20+ Interactive
Tools

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8.3k CPU
Cores

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52 TB of
RAM

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GPU Cards

Domain-centric Galaxy subdomains: Workflow4Metabolomics, ProteoRE, Covid19, Metabarcoding, Met4J, MNHN, Ecology, Plants-Pathogens

TiaaS: Since February, 2022

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80 Events

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1.9k+ taught
Students

## Support

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Online by the
community

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## Team

<figure><img src="image_41.png" /><figcaption>Cléa
Siguret</figcaption></figure>

<figure><img src="image_42.png" /><figcaption>Thomas
Chaussepied</figcaption></figure>

<figure><img src="image_43.png" /><figcaption>Romane
Libouban</figcaption></figure>

<figure><img src="image_44.png" /><figcaption>Eva
Mercier</figcaption></figure>

<figure><img src="image_45.png" /><figcaption>Julien
Seiler</figcaption></figure>

<figure><img src="image_46.png" /><figcaption>Bérénice
Batut</figcaption></figure>

<figure><img src="image_47.png" /><figcaption>Gildas Le
Corguillé</figcaption></figure>

<figure><img src="image_48.png" /><figcaption>Anthony
Bretaudeau</figcaption></figure>
<figure><img src="image_49.png" /></figure>

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Infrastructure as Code

- Galaxy project Ansible roles

- GitLab.com repos with CI
  gitlab.com/ifb-elixirfr

- 3 infrastructures: dev, preprod and prod

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ANSIBLE

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CI/CD

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usegalaxy.fr

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Sous-groupes et projets

Projets partagés

Inactif

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Search (3 character minimum)

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Nom

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cvmfs-stratum1

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data_manager

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galaxy

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Fork of the Galaxy repository including code changes that have not been me...

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galaxy_transfert

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galaxycat

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An online catalog for Galaxy instances and tools

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howto-admin

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How to administer usegalaxy.fr

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infrastructure

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Ansible playbooks and custom roles to deploy the usegalaxy.fr infrastructur...

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tools

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Ansible playbooks to manage tools on usegalaxy.fr subdomains

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welcome

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Welcome page for usegalaxy.fr base and subdomains https://usegalaxy-fr.gi...

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workflows tests

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Differents workflows are tested with planemo.

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IFB

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## Embracing Galaxy best practices:

<table><tr><td>Federated auth</td><td>LS LOGIN</td><td>✔</td></tr><tr><td>Sub-domains</td><td></td><td>✔</td></tr><tr><td>Training</td><td>TlaaS Available on these Galaxies</td><td>✔</td></tr><tr><td>CVMFS: Reference Data, Apptainer</td><td></td><td>✔</td></tr><tr><td>Tools: GxITs, Apptainer, GPUs</td><td></td><td>✔</td></tr><tr><td>Total Perspective Vortex</td><td></td><td>✔</td></tr><tr><td>PULSAR</td><td></td><td>✔</td></tr><tr><td>Homepage on Galaxy COMMUNITY HUB</td><td></td><td>✔</td></tr><tr><td>Monitoring on status.galaxyproject.org</td><td></td><td>✔</td></tr></table>

Loose requirements to be considered part of the usegalaxy.* group:

<table><tr><td>Updated</td><td>✔</td></tr><tr><td>Freely accessible</td><td>✔</td></tr><tr><td>Public infrastructure configuration</td><td>✔</td></tr><tr><td>Common Tools & Reference Data</td><td>✔</td></tr><tr><td>Functional</td><td>✔</td></tr></table>

⇒ .fr on galaxyproject.org/use/ ✔
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# Galaxy Working Group v2.0

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Galaxy

wg

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## Objectives:

1. Meeting every 2 months

2. Connect Galaxy users, developers, admins across France

3. Share knowledge (ELIXIR, Galaxy Community, etc)

4. Support UseGalaxy.fr

5. Combat misconceptions about Galaxy within the French scientific community

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4 Wm
ABRomics
ANTIBIORÉSISTANCE
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Still a rich Galaxy ecosystem but with subdomains in UseGalaxy.fr

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☑ So far, 6 small scale instances have migrated

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Galaxy
FRANCE

Autonomous, guided, migration by the users themselves

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4
Wm
Workflows-Metabolomics
ABRomics
ANTIBIORÉSISTANCE
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Recognition as a national resource (IFB roadmap, ELIXIR-FR SDP)

Contact point between French and International communities (WG 2.0)

Supports funded projects

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eosc

EuroScienceGateway

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atlasea

Trainings (national, regional, masters, ...)
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## Key Usage Indicators

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### IDC

- More Apptainer, more TPV

ABRomics
ANTIBIORESISTANCE

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- CVMFS stratus 1

- Tools/subdomains synchronisation

eosc | EuroScienceGateway

atlasea

- Pulsar nodes, smart scheduling

- SIGs (genome annotation, metagenomics, ...)

## etc etc etc

## (Galaxie codebase | French translation)

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```python
def traiter_les_résultats(soitmême, données_de_sortie: Dictionnaire[chaine, JeuDeDonnéesDeSortie]) -> Rien:
    # Croissant, bonjour
    tables_de_données_des_outils = soitmême.gestionnaires_de_données.Application.tables_de_données_des_outils
    options = OptionsDeTraitementDuMachin(
        quoi=f"data manager '{soitmême.identifiant}'",
        chemin_du_gestionnaire_de_données=soitmême._chemin_du_gestionnaire_de_données,
        fichier_de_configuration_cible=soitmême.gestionnaires_de_données.nom_de_fichier,
    )
```
Merci !

(bonjour, croissants, lapins)

Team

<figure><img src="image_103.png" /><figcaption>Cléa
Siguret</figcaption></figure>

<figure><img src="image_104.png" /><figcaption>Thomas
Chaussepied</figcaption></figure>

<figure><img src="image_105.png" /><figcaption>Romane
Libouban</figcaption></figure>

<figure><img src="image_106.png" /><figcaption>Eva
Mercier</figcaption></figure>

<figure><img src="image_107.png" /><figcaption>Julien
Seiler</figcaption></figure>

<figure><img src="image_108.png" /><figcaption>Bérénice
Batut</figcaption></figure>

<figure><img src="image_109.png" /><figcaption>Gildas Le
Corguillé</figcaption></figure>

<figure><img src="image_110.png" /><figcaption>Anthony
Bretaudeau</figcaption></figure>