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Usegalaxy.fr

https://frama.link/ifb-ag20-usegalaxyfr

AG IFB 2020

Gildas Le Corguillé, Julien Seiler, Anthony Bretaudau

David Christiany et la TaskForce IFB NNCR Cluster

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Service offered to you, the user!

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Welcome to usegalaxy.fr

Hosted by the IFB Core Cluster : 4300 CPU / 20 TB of RAM

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ELIXIR AAI authentification

100 GB for registered users - more on demand

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Ready to host your training session with a dedicated submission SLURM

All the datasets are already available as Data Libraries

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End user support - One place to get help https://community.france-bioinformatique.fr/

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New (11/2020) Galaxy Interactive Tools

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Available Tools on usegalaxy.fr

  • 1175 tools from tools - regularly up-to-date
  • Sorted by thematic sections
    • General
    • Genomic (RNASeq, DNASeq, ChipSeq …)
    • Metagenomics
    • Population Genetics
    • Metabolomics (Workflow4Metabolomics)
    • Proteomics (ProteoRE)

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  • 37 databank indexes synced with http://datacache.galaxyproject.org/

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  • Main tools weekly tested with workflows

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One instance, some sub-domains

<sub-domain>.usegalaxy.fr

  • What is a sub-domain ?
    • same infrastructure (IFB Core Cluster)
    • specific welcome page
    • sub tool panel with specific tools only
    • transferred users can find the same interface

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usegalaxy.fr

AG IFB, 26/11/2020, chacun chez soi mais l’IFB pour tous

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One instance, some sub-domains

<sub-domain>.usegalaxy.fr

  • What is a sub-domain ?
    • same infrastructure (IFB Core Cluster)
    • specific welcome page
    • sub tool panel with specific tools only
    • transferred users can find the same interface

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  • 2 sub-domains for now

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  • Easy to add new subdomain
    • Next : ngs.usegalaxy.fr (Galaxeast)

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For you the g33k!

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Contribute

https://gitlab.com/ifb-elixirfr/usegalaxy-fr

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  • Everything is managed by
  • Tasks are launched by

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  • Ask to be added to the contributor list

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  • You will be able to:
    • Access all usegalaxy.fr gitlab repositories
    • Configure Galaxy
    • Add tools
    • Add/run data manager
    • Update sub-domain welcome pages

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Contribute - add a tool

https://gitlab.com/ifb-elixirfr/usegalaxy-fr/tools

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  • Add tools in proper .yml.lock file
    • git or via the gitlab web IDE
  • Commit and make a merge request
  • Validation by our team
  • Tools automatically installed
  • Tool panel automatically sorted
    • based on yaml files

In short:

  • Fast and easy way to add tools
  • In a secure way, since reviewed by our team
  • Tools added for main and concerned subdomain

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usegalaxy.fr - TODO list

  • Interactive tools (Shiny app, Jupyter notebook, RStudio)
    • Need some rather complex settings: docker, dns, ssl, slurm …
    • Adapted to Singularity

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  • CVMFS - CernVM File System
    • Enable the Galaxy project CVMFS directory
    • Use their content in order to align usegalaxy.fr to usegalaxy.*
    • Provide Stratum1 mirrors

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  • Pulsar network - wide job execution system distributed across the world
    • Be part this network
    • Offer IFB computing resources to usegalaxy.eu

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  • TIaaS - Training Infrastructure as a Service

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End user support

One place to get help https://community.france-bioinformatique.fr/

  • Based on discourse
    • open source discussion platform�
  • Originally only for cluster related issues�
  • Now also for Scientific support, RSAT, �ProteoRE, Worflow4Metabolomics and �Galaxy related issues

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One place to help

  • 11 expert teams

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The usegalaxy.fr team is hiring:

Tasks:

  • Develop and maintain the Galaxy instance
  • Toward a better integration with usegalaxy.*
  • End-user helpdesk

Skills:

  • Good knowledge in Dev/Ops - Ansible/CI
  • Bioinformatics would be a plus
  • English speaker (better than the national average)

Salary: IE++

Location: Roscoff*, Strasbourg*, Rennes*

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Task force members

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Gildas

Le Corguillé

Julien Seiler

Anthony Bretaudau

Lain Pavot

David Christiany

12/2019 - 08/2020

François Gerbes

Didier Laborie

Nicole Charrière

David Benaben

Jean-Christophe Haessig

Guillaume Seith

usegalaxy.fr

IFB NNCR

Cluster

AG IFB, 26/11/2020, chacun chez soi mais l’IFB pour tous