BiaPy

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Collection\nInput the test data"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nInput a BiaPy YAML configuration file"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Collection\nInput the image ground truth"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Build a workflow with BiaPy"];
  1 -->|output| 3;
  2 -->|output| 3;
  0 -->|output| 3;
  40a9aa77-8541-4b12-91e6-a6e98af013ea["Output\npredictions_post_proc"];
  3 --> 40a9aa77-8541-4b12-91e6-a6e98af013ea;
  style 40a9aa77-8541-4b12-91e6-a6e98af013ea stroke:#2c3143,stroke-width:4px;
  4["Render 3-D image data"];
  0 -->|output| 4;
  3 -->|predictions_post_proc| 4;
  07011470-6b7a-4460-8e2b-728b08c1e77d["Output\nhtml"];
  4 --> 07011470-6b7a-4460-8e2b-728b08c1e77d;
  style 07011470-6b7a-4460-8e2b-728b08c1e77d stroke:#2c3143,stroke-width:4px;

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

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. 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”
4. 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/imaging/tutorials/biapy/workflows/BiaPy.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