Mapping And Molecular Identification Of Phenotype Causing Mutations

Run Workflow in Galaxy

• Galaxy Australia
• Galaxy Europe
• Galaxy France
• Galaxy Main
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nA. thaliana TAIR10 ref genome"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\naligned reads from outcrossed F2 pool"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\naligned reads from Ler mapping strain"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["SnpEff Download"];
  4["Replace parts of text"];
  0 -->|output| 4;
  5["MiModD Variant Calling"];
  4 -->|outfile| 5;
  2 -->|output| 5;
  1 -->|output| 5;
  6["MiModD Extract Variant Sites"];
  5 -->|ofile| 6;
  7["MiModD NacreousMap"];
  6 -->|output_vcf| 7;
  8["MiModD VCF Filter"];
  6 -->|output_vcf| 8;
  9["SnpEff"];
  8 -->|outputfile| 9;
  3 -->|snpeff_db| 9;
  10["MiModD Report Variants"];
  9 -->|snpeff_output| 10;

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Hands-on: Importing a workflow

• Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
• Click on galaxy-upload Import at the top-right of the screen
• Provide your workflow
  • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
  • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
• Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/mapping-by-sequencing/workflows/workflow-arabidopsis.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows