GO Enrichment Workflow

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\nGO annotations Drosophila melanogaster"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nGO"];
  style 1 stroke:#2c3143,stroke-width:4px;
  10["Filter"];
  2 -->|output| 10;
  11["GOEnrichment"];
  3 -->|output| 11;
  1 -->|output| 11;
  4 -->|output| 11;
  5 -->|output| 11;
  12["GOEnrichment"];
  3 -->|output| 12;
  1 -->|output| 12;
  4 -->|output| 12;
  5 -->|output| 12;
  13["GOSlimmer"];
  3 -->|output| 13;
  1 -->|output| 13;
  6 -->|output| 13;
  14["GOEnrichment"];
  3 -->|output| 14;
  1 -->|output| 14;
  4 -->|output| 14;
  7 -->|output| 14;
  15["GOEnrichment"];
  3 -->|output| 15;
  1 -->|output| 15;
  4 -->|output| 15;
  8 -->|output| 15;
  16["GOEnrichment"];
  0 -->|output| 16;
  1 -->|output| 16;
  2 -->|output| 16;
  9 -->|out_file1| 16;
  17["GOEnrichment"];
  0 -->|output| 17;
  1 -->|output| 17;
  10 -->|out_file1| 17;
  9 -->|out_file1| 17;
  18["GOEnrichment"];
  13 -->|output| 18;
  6 -->|output| 18;
  4 -->|output| 18;
  5 -->|output| 18;
  2["ℹ️ Input Dataset\ntrapnellPopulation.tab"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nGO annotations Mus musculus"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nMouse population"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nMouse diff"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["ℹ️ Input Dataset\nGO Slim"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["ℹ️ Input Dataset\nmouseUnderexpressed.txt"];
  style 7 stroke:#2c3143,stroke-width:4px;
  8["ℹ️ Input Dataset\nmouseOverexpressed.txt"];
  style 8 stroke:#2c3143,stroke-width:4px;
  9["Filter"];
  2 -->|output| 9;

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/transcriptomics/tutorials/goenrichment/workflows/goenrichment-workflow.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