Heatmap2 Workflow

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nDE results"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nnormalized counts"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nheatmap genes"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Filter"];
  0 -->|output| 3;
  4["Join two Datasets"];
  2 -->|output| 4;
  1 -->|output| 4;
  5["Filter"];
  3 -->|out_file1| 5;
  6["Cut"];
  4 -->|out_file1| 6;
  7["Sort"];
  5 -->|out_file1| 7;
  8["Sort"];
  5 -->|out_file1| 8;
  9["Transpose"];
  6 -->|out_file1| 9;
  10["Select first"];
  7 -->|outfile| 10;
  11["Select first"];
  8 -->|outfile| 11;
  12["Select last"];
  8 -->|outfile| 12;
  13["heatmap2"];
  9 -->|out_file| 13;
  3145c334-6741-4bc9-8376-fb7eff8b9045["Output\nheatmap custom genes"];
  13 --> 3145c334-6741-4bc9-8376-fb7eff8b9045;
  style 3145c334-6741-4bc9-8376-fb7eff8b9045 stroke:#2c3143,stroke-width:4px;
  14["Join two Datasets"];
  10 -->|out_file1| 14;
  1 -->|output| 14;
  15["Concatenate datasets"];
  11 -->|out_file1| 15;
  12 -->|out_file1| 15;
  16["Sort"];
  14 -->|out_file1| 16;
  17["Cut"];
  14 -->|out_file1| 17;
  18["Join two Datasets"];
  15 -->|out_file1| 18;
  1 -->|output| 18;
  19["Cut"];
  16 -->|outfile| 19;
  20["heatmap2"];
  17 -->|out_file1| 20;
  ac189295-2211-41b1-8f9c-d92d24ba1cac["Output\nheatmap top 20 genes"];
  20 --> ac189295-2211-41b1-8f9c-d92d24ba1cac;
  style ac189295-2211-41b1-8f9c-d92d24ba1cac stroke:#2c3143,stroke-width:4px;
  21["heatmap2"];
  17 -->|out_file1| 21;
  22["Cut"];
  18 -->|out_file1| 22;
  23["heatmap2"];
  19 -->|out_file1| 23;
  24["heatmap2"];
  22 -->|out_file1| 24;

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/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/workflows/rna-seq-viz-with-heatmap2.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