Circos for E. Coli

visualisation-circos-microbial/main-workflow

Author(s)
Helena Rasche
Version
1
Last updated
Nov 8, 2023
License
AGPL-3.0-or-later
Tags
name:circos
name:viz

Features
Tutorial
Ploting a Microbial Genome with Circos
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00273
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
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;

Inputs

Input Label
Input dataset Genome
Input dataset Genes
Input dataset RNA Seq Coverage (1)
Input dataset RNA Seq Coverage (2)
Input dataset DNA Sequencing Coverage
Input dataset Variants

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy9 Circos

Tools

Tool Links
Cut1
gff2bed1
toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy9 View in ToolShed

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

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:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
1 42fa4f8af 2023-11-03 13:29:10 add circos microbial tutorial

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