Workflow Constructed From History 'Heinz Workflow Trial Sep 11'

transcriptomics-network-analysis-with-heinz/galaxy-workflow-heinz

Author(s)

Version
3
Last updated
Jan 23, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
transcriptomics

Features
Tutorial
Network analysis with Heinz
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00243
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\nEdge File"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nInput dataset collection"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Collection\nInput dataset collection"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["DESeq2"];
  1 -->|output| 3;
  2 -->|output| 3;
  4["Cut"];
  3 -->|deseq_out| 4;
  5["Cut"];
  3 -->|deseq_out| 5;
  6["Fit a BUM model"];
  4 -->|out_file1| 6;
  7["Calculate a Heinz score"];
  5 -->|out_file1| 7;
  6 -->|dist_params| 7;
  8["Identify optimal scoring subnetwork"];
  7 -->|score| 8;
  0 -->|output| 8;
  9["Visualize"];
  8 -->|subnetwork| 9;

Inputs

Input Label
Input dataset Edge File
Input dataset collection
Input dataset collection

Outputs

From Output Label

Tools

Tool Links
Cut1
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz/1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_bum/1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_scoring/1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_visualization/0.1.0 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
3 667ff3de9 2020-01-22 10:59:29 annotation
2 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
1 6a6b3b2cf 2018-10-10 11:42:48 Renamed the folder, rewrote the key points; added tags; added a paragraph in the end to correspond to the research question in this tutorial.

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/network-analysis-with-heinz/workflows/Galaxy-Workflow-Heinz.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