Circos for E. Coli

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nGenome"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nGenes"];
  style 1 stroke:#2c3143,stroke-width:4px;
  10["Circos: bigWig to Scatter"];
  3 -->|output| 10;
  11["Circos: bigWig to Scatter"];
  4 -->|output| 11;
  12["Cut"];
  5 -->|output| 12;
  13["Circos: bigWig to Scatter"];
  6 -->|output| 13;
  14["Circos: Interval to Tiles"];
  8 -->|out_file1| 14;
  15["Circos"];
  0 -->|output| 15;
  10 -->|output| 15;
  12 -->|out_file1| 15;
  9 -->|output| 15;
  11 -->|output| 15;
  7 -->|output| 15;
  14 -->|output| 15;
  14 -->|output| 15;
  13 -->|output| 15;
  ad540557-b836-4f68-9d64-7132c059c53e["Output\nplot"];
  15 --> ad540557-b836-4f68-9d64-7132c059c53e;
  style ad540557-b836-4f68-9d64-7132c059c53e stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nRNA Seq Coverage 1"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nRNA Seq Coverage 2"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nDNA Sequencing Coverage"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nVariants"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["GC Skew"];
  0 -->|output| 6;
  7["Circos: Interval to Circos Text Labels"];
  1 -->|output| 7;
  8["GFF-to-BED"];
  1 -->|output| 8;
  9["Circos: bigWig to Scatter"];
  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/visualisation/tutorials/circos-microbial/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