Diploid

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nGIAB-Ashkenazim-Trio-hg19.bam"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["SnpEff Download"];
  2["ℹ️ Input Dataset\nGIAB-Ashkenazim-Trio.tabular"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["FreeBayes"];
  0 -->|output| 3;
  4["VcfAllelicPrimitives:"];
  3 -->|output_vcf| 4;
  5["SnpEff eff:"];
  4 -->|out_file1| 5;
  1 -->|snpeff_db| 5;
  6["GEMINI load"];
  5 -->|snpeff_output| 6;
  2 -->|output| 6;
  7["GEMINI_db_info"];
  6 -->|outfile| 7;
  8["GEMINI_query2"];
  6 -->|outfile| 8;
  9["GEMINI_query1"];
  6 -->|outfile| 9;

Inputs

Outputs

Tools

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/dip/workflows/diploid.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