MuSiC-Deconvolution: Compare

single-cell-bulk-music-4-compare/compare

Author(s)
Wendi Bacon, Mehmet Tekman
Version
1
Last updated
Jan 20, 2023
License
None Specified, defaults to CC-BY-4.0
Tags
name:singlecell
name:transcriptomics
name:training

Features
Tutorial
Comparing inferred cell compositions using MuSiC deconvolution
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00190
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\nESet Object - Single cell:T2D"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nESet Object - Single cell:normal"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nESet Object - Bulk:normal"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nESet Object - Bulk:T2D"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nESet Object - Single cell Total"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["MuSiC Compare: Like with like"];
  2 -->|output| 5;
  1 -->|output| 5;
  3 -->|output| 5;
  0 -->|output| 5;
  6["MuSiC Compare: healthyscref"];
  2 -->|output| 6;
  3 -->|output| 6;
  1 -->|output| 6;
  7["MuSiC Compare - Altogether"];
  2 -->|output| 7;
  3 -->|output| 7;
  4 -->|output| 7;

Inputs

Input Label
Input dataset ESet Object - Single cell:T2D
Input dataset ESet Object - Single cell:normal
Input dataset ESet Object - Bulk:normal
Input dataset ESet Object - Bulk:T2D
Input dataset ESet Object - Single cell Total

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/bgruening/music_compare/music_compare/0.1.1+galaxy4 MuSiC Compare MuSiC Compare: Like with like
toolshed.g2.bx.psu.edu/repos/bgruening/music_compare/music_compare/0.1.1+galaxy4 MuSiC Compare MuSiC Compare: healthyscref
toolshed.g2.bx.psu.edu/repos/bgruening/music_compare/music_compare/0.1.1+galaxy4 MuSiC Compare MuSiC Compare - Altogether

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/music_compare/music_compare/0.1.1+galaxy4 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 9a561b375 2022-11-27 20:30:42 update workflows

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music-4-compare/workflows/compare.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