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This course introduces the 2 commonly used workflow managers in the South Green Bioformatics platform, both in a theoretical and practical way, with hands-on practice sessions. It will help you to quickly develop and run your own pipelines using these tools through an graphical user or command-line interface.

TOGGLe, a flexible framework for easily building complex workflows and performing robust large-scale NGS analyses Christine Tranchant-Dubreuil, Sebastien Ravel, Cecile Monat, Gautier Sarah, Abdoulaye Di- allo, Laura Helou, Alexis Dereeper, Ndomassi Tando, Julie Orjuela-Bouniol, Francois Sabot. bioRxiv https: //www.biorxiv.org/content/early/2018/01/10/245480.

TOGGle website

Galaxy website

Prerequisites

Prior knowledge of workflow managers not necessary Basic knowledge of Linux (Linux for dummies required) - TOGGLe practical

Program

  • Why using a workflow manager to analyse data ?
  • How to perform an analysis ?
  • How to create your own workflow ?
  • How to execute it?
  • Use case

Learning objectives

  • Explaining what Workflow Managers are,
    in which way they differ from each other.
  • How you can use them in your research.
  • Creating your own workflow
  • Analysing your NGS data with Galaxy and TOGGLe

Training material

  • Slides workflow managers : see
  • Slides galaxy : see
  • Slides TOGGLe : see
  • Slides GIGWA : see
  • Practice Galaxy : see
  • Practice TOGGLe : see

Instructors

  • Alexis Dereeper (AD) - alexis.dereeper@ird.fr
  • Sebastien Ravel (SR) - sebastien.ravel@cirad.fr
  • Julie Orjuela (JO) - julie.orjuela@ird.fr
  • Christine Tranchant (CT) - christine.tranchant@ird.fr

Trainings

Date Location Topics Participants Instructors Links Units
2019 Montpellier, France TOGGLe 15 AD, SR, CT, JO   UMR DIADE, IPME, MIVEGEC, INTERTRYP, AGAP
2018 Montpellier, France TOGGLe 20 AD, SR, CT   UMR DIADE, IPME, MIVEGEC, INTERTRYP, AGAP
2017 Montpellier, France TOGGLe 20 CT, AD   UMR DIADE, IPME, MIVEGEC, INTERTRYP