Trainings 2019 – Galaxy Practice

Galaxy Practice

Description Hands On Lab Exercises for Galaxy
Related-course materials Galaxy introduction
Authors Alexis Dereeper (
Creation Date 15/03/2018
Last Modified Date 15/03/2018


Practice 1 : Basics of Galaxy (by Galaxy team)

Practice1 will be performed in the Galaxy main -
Practice1 consists of following the "Galaxy 101" hands-on provided by Galaxy team

Practice 2 : How to import datasets

Practice2 will be performed in the Galaxy South Green.

  • Connect to Galaxy South Green -
  • Log in using account
  • Rename your history "test data upload"

Test the different ways to import datasets into your history:

  • Copy/paste the content of a dataset
  • Copy/paste the link/URL of an external file to be imported -
  • Upload any txt file from your local computer
  • Use FTP procedure to upload big file following the procedure described form Galaxy homepage
  • Import a dataset from a shared data library

Practice 3 : Concrete application: From reads to SNPs

Practice3 will be performed in the Galaxy South Green.

  • Create a new history for this practice (ex: SNP calling)
  • From Shared data => Data libraries, import into your history fastq datasets for 3 individuals (RC1, RC2, RC3) as well as reference fasta
    Galaxy_trainings_2015 => NGS
  • Check these 6 files and create a collection of 3 dataset pairs Build a list of dataset pairs. Associate files by pair and give a name to your collection
  • Process a FastqC analysis for RC1 to control the quality of sequencing
  • Import the shared workflow called Mapping_SNPCalling_PairedEnd
  • Observe the different steps of the workflow
  • Run the complete workflow. It provides a collection of Bam files.
  • Observe the final VCF output



The resource material is licensed under the Creative Commons Attribution 4.0 International License (here).