Music: Pre-grouping cell types

Run Workflow in Galaxy

• Galaxy Main
• Galaxy Europe
• Galaxy France
• Galaxy Australia
• 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 Dataset\nBulk RNA Assay Tabular"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nBulk RNA Phenotype Tabular"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nepith.markers"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nimmune.markers"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["Construct Expression Set Object"];
  0 -->|output| 6;
  1 -->|output| 6;
  7["Construct Expression Set Object"];
  2 -->|output| 7;
  3 -->|output| 7;
  8["MuSiC Deconvolution"];
  7 -->|out_rds| 8;
  6 -->|out_rds| 8;
  9c4e9980-be47-4095-b116-5c6874329f63["Output\nout_pdf"];
  8 --> 9c4e9980-be47-4095-b116-5c6874329f63;
  style 9c4e9980-be47-4095-b116-5c6874329f63 stroke:#2c3143,stroke-width:4px;
  9["MuSiC Deconvolution"];
  7 -->|out_rds| 9;
  4 -->|output| 9;
  5 -->|output| 9;
  6 -->|out_rds| 9;
  3935b7f2-a422-4ad8-bbe2-65615865174b["Output\nout_tab"];
  9 --> 3935b7f2-a422-4ad8-bbe2-65615865174b;
  style 3935b7f2-a422-4ad8-bbe2-65615865174b stroke:#2c3143,stroke-width:4px;
  a002d52f-2253-4763-852e-6fe3ef90d352["Output\nout_pdf"];
  9 --> a002d52f-2253-4763-852e-6fe3ef90d352;
  style a002d52f-2253-4763-852e-6fe3ef90d352 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

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. 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”
4. 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/music_pre-grouping_cell_types.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