Circos tutorial

visualisation-circos/main-workflow

Author(s)
Helena Rasche, Saskia Hiltemann
Version
7
Last updated
May 15, 2023
License
AGPL-3.0-or-later
Tags
visualisation

Features
Tutorial
Visualisation with Circos
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00271
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\nInput dataset"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Remove beginning"];
  2["Remove beginning"];
  3["Select"];
  4["Circos"];
  5["Cut"];
  1 -->|out_file1| 5;
  6["Select random lines"];
  2 -->|out_file1| 6;
  7["Cut"];
  3 -->|out_file1| 7;
  8["Select random lines"];
  5 -->|out_file1| 8;
  9["Circos"];
  0 -->|output| 9;
  7 -->|out_file1| 9;
  10["Circos"];
  0 -->|output| 10;
  7 -->|out_file1| 10;
  11["Circos"];
  0 -->|output| 11;
  7 -->|out_file1| 11;
  8 -->|out_file1| 11;
  12["Circos"];
  0 -->|output| 12;
  7 -->|out_file1| 12;
  8 -->|out_file1| 12;
  13["Circos"];
  0 -->|output| 13;
  7 -->|out_file1| 13;
  8 -->|out_file1| 13;
  14["Circos"];
  0 -->|output| 14;
  7 -->|out_file1| 14;
  8 -->|out_file1| 14;
  15["Circos"];
  0 -->|output| 15;
  7 -->|out_file1| 15;
  8 -->|out_file1| 15;
  6 -->|out_file1| 15;
  16["Circos"];
  0 -->|output| 16;
  7 -->|out_file1| 16;
  8 -->|out_file1| 16;
  6 -->|out_file1| 16;

Inputs

Input Label
Input dataset

Outputs

From Output Label

Tools

Tool Links
Cut1
Grep1
Remove beginning1
random_lines1
toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy12 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
10 9171ba4a5 2023-05-15 14:56:12 add license, creators
9 5cb78929f 2023-05-15 14:39:24 bump circos versions
8 b267c0f28 2021-01-21 22:51:33 Circos tutorial papercuts v3
7 fdc5b8d63 2021-01-21 22:39:44 Circos tutorial papercuts v2
6 08953e54d 2021-01-21 21:49:05 Circos tutorial papercuts
5 cf8b1cb05 2020-08-31 01:11:11 Update some workflow names for consistency
4 667ff3de9 2020-01-22 10:59:29 annotation
3 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
2 7da80b341 2020-01-10 14:56:15 Workflows fix
1 e80b7c41c 2018-10-19 14:26:19 wip

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/visualisation/tutorials/circos/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