Workflows

These workflows are associated with Ploting a Microbial Genome with Circos

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.

Circos for E. Coli
Helena Rasche

Last updated Nov 3, 2023

Launch in Tutorial Mode
License: AGPL-3.0-or-later
Tests: ✅ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy Australia Galaxy Main Galaxy Europe Galaxy France 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;

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
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 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: