MuSiC Workflow

Run Workflow in Galaxy

• Galaxy Australia
• Galaxy France
• Galaxy Europe
• Galaxy Main
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nscRNA Assay Tabular"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nscRNA Phenotype Tabular"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Parameter\nscRNA Metadata"];
  style 2 fill:#ded,stroke:#393,stroke-width:4px;
  3["ℹ️ Input Dataset\nBulk RNA Assay Tabular"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Parameter\nBulk RNA Annotation"];
  style 4 fill:#ded,stroke:#393,stroke-width:4px;
  5["ℹ️ Input Parameter\nCell Types List"];
  style 5 fill:#ded,stroke:#393,stroke-width:4px;
  6["ℹ️ Input Dataset\nCell Markers C1"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["ℹ️ Input Dataset\nCell Markers C2"];
  style 7 stroke:#2c3143,stroke-width:4px;
  8["Construct scRNA ESet Object"];
  0 -->|output| 8;
  2 -->|output| 8;
  1 -->|output| 8;
  872b3dd2-322c-47cc-b5b9-071a9f939320["Output\nConstruct Expression Set Object on input dataset(s): RData ESet Object"];
  8 --> 872b3dd2-322c-47cc-b5b9-071a9f939320;
  style 872b3dd2-322c-47cc-b5b9-071a9f939320 stroke:#2c3143,stroke-width:4px;
  9["Construct Bulk RNA ESet Object"];
  4 -->|output| 9;
  3 -->|output| 9;
  10["Extract Cell Types"];
  8 -->|out_rds| 10;
  11["Extract General Info"];
  8 -->|out_rds| 11;
  1733593f-847d-4adb-91f4-fd78c077b074["Output\nInspect Expression Set Object on input dataset(s): Inspection Result"];
  11 --> 1733593f-847d-4adb-91f4-fd78c077b074;
  style 1733593f-847d-4adb-91f4-fd78c077b074 stroke:#2c3143,stroke-width:4px;
  12["Extract General Info Bulk"];
  9 -->|out_rds| 12;
  13["Music: Estimate Cell Proportions"];
  9 -->|out_rds| 13;
  5 -->|output| 13;
  8 -->|out_rds| 13;
  14["Music: Compute Dendrogram"];
  9 -->|out_rds| 14;
  6 -->|output| 14;
  7 -->|output| 14;
  8 -->|out_rds| 14;
  df2e83a5-ac67-460f-8b0f-ac3f3b63280f["Output\nMuSiC on input dataset(s): PDF Plots"];
  14 --> df2e83a5-ac67-460f-8b0f-ac3f3b63280f;
  style df2e83a5-ac67-460f-8b0f-ac3f3b63280f stroke:#2c3143,stroke-width:4px;

Inputs

Outputs

Tools

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

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 galaxy-upload 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:

Version History

For Admins

Installing the workflow tools

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