Final - Modeling Breast Cancer Subtypes (flexynesis only)

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nclin_train"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nclin_test"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\ngex_train"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\ngex_test"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\ncna_train"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\ncna_test"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6[" Flexynesis niter1"];
  5 -->|output| 6;
  4 -->|output| 6;
  1 -->|output| 6;
  3 -->|output| 6;
  0 -->|output| 6;
  2 -->|output| 6;
  a3d336d0-14da-4688-8f20-9fbe4a3745a5["Output\nniter1 flexynesis output"];
  6 --> a3d336d0-14da-4688-8f20-9fbe4a3745a5;
  style a3d336d0-14da-4688-8f20-9fbe4a3745a5 stroke:#2c3143,stroke-width:4px;
  7[" Flexynesis niter5"];
  5 -->|output| 7;
  4 -->|output| 7;
  1 -->|output| 7;
  3 -->|output| 7;
  0 -->|output| 7;
  2 -->|output| 7;
  d3447b34-1233-4c77-a348-387e5e021782["Output\nniter5 flexynesis output"];
  7 --> d3447b34-1233-4c77-a348-387e5e021782;
  style d3447b34-1233-4c77-a348-387e5e021782 stroke:#2c3143,stroke-width:4px;
  8["Extract prediction table - niter1"];
  6 -->|results| 8;
  9["Extract test embeddings - niter1"];
  6 -->|results| 9;
  10["Extract prediction table - niter5"];
  7 -->|results| 10;
  11["Extract test embeddings - niter5"];
  7 -->|results| 11;
  12["Sort"];
  8 -->|output| 12;
  13["Sort"];
  10 -->|output| 13;
  14["Flexynesis plot"];
  9 -->|output| 14;
  12 -->|outfile| 14;
  a132b519-38f8-4d0a-af84-4343a24a1f7a["Output\nembedding plot umap - niter1"];
  14 --> a132b519-38f8-4d0a-af84-4343a24a1f7a;
  style a132b519-38f8-4d0a-af84-4343a24a1f7a stroke:#2c3143,stroke-width:4px;
  15["UMAP plot on test embeddings"];
  11 -->|output| 15;
  13 -->|outfile| 15;
  bd28d5e9-97ed-419e-b4e6-0e31eef2db18["Output\nembedding plot umap - niter5"];
  15 --> bd28d5e9-97ed-419e-b4e6-0e31eef2db18;
  style bd28d5e9-97ed-419e-b4e6-0e31eef2db18 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/statistics/tutorials/flexynesis_classification/workflows/main_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