ELIXIR Galaxy Workshop

at Roscoff

23th - 26th April 2019

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Hosted by

ELIXIR Galaxy Community

Björn Grüning, Frederik Coppens, Gildas Le Corguillé

et al.

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www.elixir-europe.org

ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559.

Galaxy

Focus on reproducible research since beginning

• Open Source
• Sharing data, tools, workflows
• Interface
• intuitive webportal for biologists
• unified API for bioinformaticians

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Broad usage

• internationally : 100 public instances, 5900 papers citing
• within ELIXIR:
• WG established in 2015
• WG survey: many small local instances aimed at biologists
• 13 Nodes supportive

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ELIXIR All Hands 2018, June 2018, Berlin, Germany

Galaxy in the context of ELIXIR

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ELIXIR All Hands 2018, June 2018, Berlin, Germany

Introduce yourself

ELIXIR Galaxy Workshop at Roscoff

Hosted by

Estelle Ancelet

Team/Lab/Institute:

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Main projects:

• Use Galaxy with our agroecosystem models (needing large computing resources) / Use workflows

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Hackathon project / Interest:

• check/correct one of our tool using conda dependencies
• check/correct one of our tool using a singularity/docker dependency
• use Continuous Integration from tool wrapping to galaxy (through planemo, tests, repository, toolshed, galaxy upgrade…)
• learn how to use GTN documentation and environment to train my team members

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Skills:

• Web development
• Python (beginner)
• Galaxy tool development with planemo and Galaxy admin (beginner)

modelling and simulating platform for agroecosystems

Bérénice Batut

bebatut

@bebatut

bebatut.fr

0000-0001-9852-1987

Team/Lab/Institute

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Main projects

• Galaxy tools (metagenomics, etc)
• Galaxy Training Material, etc

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Hackathon project / Interest

• Galaxy Training Material: mentoring, new material
• Galaxy tool development: help, review

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Skills

• Galaxy Training Material
• Galaxy tool development: conda, Planemo
• Git, Python, R

Simon Bénateau

Team/Lab/Institute: Muséum national d'Histoire naturelle, Centre

d'Ecologie et des Sciences de la Conservation

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Main projects: Galaxy-E, Galaxy-Bricks

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Hackathon project / Interest:

• Developing tools and training material for non professional

scientists (citizen science) and high school students.

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Skills:

• Data analysis, R

Anthony Bretaudeau

Team/Lab/Institute: GenOuest / BIPAA, INRA, Rennes, France

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Main projects:

• Insect Genomics
• Galaxy Genome Annotation (Galaxy+GMOD)
• Admin of (bipaa-)galaxy.genouest.org (+ cluster)

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Hackathon project / Interest:

• Review/Improve annotation training material
• Help on tool dev / training material / *

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Skills:

• Galaxy tool development: Conda, Planemo
• Git, Python
• Sys admin
• Training Material
• Bunnies

https://orcid.org/0000-0003-0914-2470

https://github.com/abretaud

https://twitter.com/abretau

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Alexandre Burel

Team/Lab/Institute: Laboratoire de Spectrométrie de Masse BioOrganique, IPHC, CNRS

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Main projects: Software development in proteomics

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Hackathon project / Interest:

• Convert existing tools to put them in the toolshed
• See limitations regarding certains types of applications

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Skills:

• Development in Java, Perl, Scala, C#, a bit of R

Etienne Camenen

Team/Lab/Institute: Institut du Cerveau et de la Moelle Épinière (iCONICS) - IFB Sorbonne Université / CNRS

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Main projects: Shiny and Galaxy interactive software for multi-source data analysis

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Hackathon project / Interest:

• Integrating the multimodal data analysis tool into the Galaxy W4M community
• Merging developments through Shiny's Dockerization and its visualization from the Galaxy interface

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Skills:

• Languages: R (Shiny), Python, JS
• Sys. admin. : Docker, Galaxy
• Git

Florence Combes

Team/Lab/Institute: CEA Grenoble : EdyP (Proteomics)

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Main projects: Proteomics (ProteoRE), R packages for proteomics analysis

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Hackathon project / Interest:

1) Tools :

Integration of one (or more) tools for the ProteoRE instance.

2) Training material :

Deployment of our training material on the dedicated Galaxy project training-material github.

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Skills:

• Bioanalysis, R, Omics data (stat)analysis, Git
• Galaxy development tools and integration tools

Romain Dallet

Team/Lab/Institute: ABiMS Station Biologique de Roscoff - IFB - CNRS

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Main projects: Workflow4Metabolomics visualizations

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Hackathon project / Interest:

• Galaxy Interactive Tours
• Galaxy Interactive Environments and Shiny visualizations

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Skills:

• Languages: R (Shiny), Python
• Sys. admin. : Docker, Galaxy
• Git

Gianluca De Moro

Team/Lab/Institute: CCMAR / Plant Systematics and Bioinformatics Research Group (PSB)

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Main projects: EOSC-Life demostrator discussion

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Hackathon project / Interest:

• Marine Eukaryote Genomics Portal – A genome annotation platform for small pelagic fishes
• Galaxy Genome Annotation (GGA)

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Skills:

• Damn! I should have bring some?

Edit by Gildas

Stephan Flemming

stephanflemming

0000-0002-4632-3863

Team/Lab/Institute

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Main projects

• Galaxy tools

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Hackathon project / Interest

• Galaxy tool development

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Skills

• Galaxy tool development
• Python, R

Anne Fouilloux

Team/Lab/Institute: University of Oslo / Geosciences

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Main projects: Development and integration of tools from geoscience and climate communities to galaxy.

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Hackathon project / Interest:

• Know how to use it and set up on local machines.
• Tools for exploring climate data (cmip) and other geo spatial data for instance from copernicus (reanalysis)

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Skills:

• Damn! I should have bring some?

Edit by Gildas

Nadia Goué

Team/Lab/Institute: Plateforme Auvergne Bioinformatics,

Mesocentre Clermont Auvergne University

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Main projects:

• admin on Galaxy instance
• establishing workflows on cluster
• training

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Hackathon project / Interest:

• learn on best practices to build and test tools (Planemo, Bioconda, Travis, …)

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Skills:

• data analysis
• Galaxy admin
• bash, R, Perl (sometimes ago), python and git (more and more)

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Björn Grüning

Team/Lab/Institute:

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Main projects: usegalaxy.eu, Galaxy Project, IUC, Bioconda, Biocontainers, and many many more …

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Hackathon project / Interest:

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Skills:

• Fetching the list ….
• Please wait ….

Edit by Gildas

Loraine Guéguen

Team/Lab/Institute: ABiMS / LBI2M Station Biologique de Roscoff - IFB

CNRS / Sorbonne University

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Main projects: Galaxy, GMOD (JBrowse, Apollo…)

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Hackathon project / Skills / Interest:

• Update some Galaxy tools
• Improve some Training Materials

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Skills:

• Tool integration / Planemo / Conda
• Git
• Training Material
• Galaxy Administration

https://github.com/loraine-gueguen

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Agnes Hotz-Wagenblatt

Team/Lab/Institute: OmicsIT and Data Management Core Facility,

German Cancer Research Center (DKFZ) in Heidelberg

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Main projects: Analysis of all kinds of Sequencing Data, establishing Workflows

• Transfer workflows from a different pipeline system to Galaxy

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Hackathon project / Interest:

• Learn to develop my own workflows in Galaxy
• Galaxy training

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Skills:

• Perl, Linux, basic R, basic Galaxy
• Analysis tools for sequencing data

https://www.dkfz.de/en/forschung/zentrale_einrichtungen/cf-omics/CF_omics.html

Yvan Le Bras

Team/Lab/Institute: Station marine de Concarneau

UMS PatriNat MNHN-CNRS-AFB

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Main projects: “Pôle national de données de biodiversité” french research infrastructure,

Galaxy-E

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Hackathon project / Skills / Interest:

• Improve / Finalize some Training Material for the Galaxy-E project
• Ecology

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Skills:

• Data analysis
• Training Material

https://orcid.org/0000-0002-8504-068X

https://github.com/yvanlebras

https://twitter.com/yvan2935

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Gildas Le Corguillé

Team/Lab/Institute: ABiMS Station Biologique de Roscoff - IFB

Sorbonne Université / CNRS

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Main projects: Workflow4Metabolomics, IFB Core Cluster

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Hackathon project / Skills / Interest:

• Improve / Finalize some Training Material for the W4M project
• Speak about usegalaxy.* admin stuff

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Skills:

• Tool integration / Planemo / Conda
• Git
• Training Material
• Galaxy Administration

https://orcid.org/0000-0003-1742-9711

https://github.com/lecorguille

https://twitter.com/glecorguille

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Valentin Loux

Team/Lab/Institute: INRA / Migale bioinformatics platform

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Main projects: Metagenomics, Proteomics (ProteoRe)

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Hackathon project / Interest:

• Networking
• Putting existing training material into the GTN
• Main topic will be proteomics but could also cover metagenomics, ngs data analysis, …
• Interested in Shiny / Galaxy integration (GIE ?)

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Skills:

• Tool integration
• Administration of a Galaxy instance in production

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https://orcid.org/0000-0002-8268-915X

http://migale.jouy.inra.fr

http://twitter.com/vloux/

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Naïra Naouar

Team/Lab/Institute: Plateforme de bioinformatique ARTbio, Sorbonne Université, IBPS

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Main projects: Analyze different NGS data using Galaxy - Galaxy Workflows

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Hackathon project / Interest:

• Tools integration in Galaxy
• Extract material & methods from a Galaxy Workflow

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Skills:

• R, Unix bash
• NGS data Analysis

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Rémi Planel

Team/Lab/Institute: Hub de Bioinformatique et de Biostatistique, C3BI, Institut Pasteur

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Main projects:

• Admin a Galaxy instance
• Web development for bioinformatics

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Hackathon project / Interest:

• Learn about Galaxy tool integration
• Learn about Galaxy admin

Skills:

• Javascript, Python, Perl
• Development web: D3.js, React, Redux
• Workflow management system: Nextflow

Stéphanie Robin

Team/Lab/Institute: GenOuest / BIPAA, INRA, Rennes, France

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Main projects:

• Insect Genomics
• Trainings

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Hackathon project / Interest:

• add new training material (smallRNAseq analysis)

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Skills:

• Data analysis
• Training Material

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Virginie Rossard

Team/Lab/Institute:

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Main projects:

• Admin a Galaxy instance (France Grille) with our chemometrics tools

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Hackathon project / Interest:

• check/correct one of our tool using conda dependencies
• check/correct one of our tool using a singularity/docker dependency
• use Continuous Integration from tool wrapping to galaxy (through planemo, tests, repository, toolshed, galaxy upgrade…)
• learn how to use GTN documentation and environment to train my team members
• Galaxy Interactive Environments (ipython and RStudio, Shiny)

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Skills:

• Web development
• Development in Python (beginner), PHP,R, Git, Unix bash
• Galaxy tool development with planemo and Galaxy admin

chemometrics software

Julien Saint-Vanne

Team/Lab/Institute: ABiMS Station Biologique de Roscoff - LABERCA

Sorbonne Université / CNRS

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Main projects: MS/MS tool integration in Workflow4Metabolomics Galaxy

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Hackathon project / Skills / Interest:

• Learn about Galaxy tool integration
• Complete my tests on Galaxy tools (Planemo, Travis, etc…)

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Skills:

• R scripts
• Git
• Galaxy uses

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https://github.com/jsaintvanne

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