MuSiC-Deconvolution: Data generation | sc | matrix + ESet

Run Workflow in Galaxy

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

flowchart TD
  0["EBI SCXA Data Retrieval"];
  1["ℹ️ Input Dataset\nSingle cell metadata"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Scanpy Read10x"];
  0 -->|barcode_tsv| 2;
  0 -->|genes_tsv| 2;
  0 -->|matrix_mtx| 2;
  6bd01730-f0b5-4824-8cfc-d563cc9c7f7d["Output\nScanpy Read10x on input dataset(s): anndata"];
  2 --> 6bd01730-f0b5-4824-8cfc-d563cc9c7f7d;
  style 6bd01730-f0b5-4824-8cfc-d563cc9c7f7d stroke:#2c3143,stroke-width:4px;
  3["Inspect AnnData"];
  2 -->|output_h5| 3;
  4["Transpose"];
  3 -->|X| 4;
  5["annotateMyIDs"];
  4 -->|out_file| 5;
  c39c7d69-550e-4b54-a412-317b599c5e55["Output\nannotateMyIDs on input dataset(s): Annotated IDs"];
  5 --> c39c7d69-550e-4b54-a412-317b599c5e55;
  style c39c7d69-550e-4b54-a412-317b599c5e55 stroke:#2c3143,stroke-width:4px;
  6["🛠️ Subworkflow\n1st step removed - Convert from Ensembl to GeneSymbol, summing duplicate genes"];
  style 6 fill:#edd,stroke:#900,stroke-width:4px;
  5 -->|out_tab| 6;
  4 -->|out_file| 6;
  7["Construct Expression Set Object"];
  6 -->|Gene Symbol Count Matrix| 7;
  1 -->|output| 7;
  e8c91df0-4e6c-4eb2-9807-c2679b494958["Output\nConstruct Expression Set Object on input dataset(s): RData ESet Object"];
  7 --> e8c91df0-4e6c-4eb2-9807-c2679b494958;
  style e8c91df0-4e6c-4eb2-9807-c2679b494958 stroke:#2c3143,stroke-width:4px;
  2912d09b-b178-4035-b7c8-7038392e2bf2["Output\nConstruct Expression Set Object on input dataset(s): General Info"];
  7 --> 2912d09b-b178-4035-b7c8-7038392e2bf2;
  style 2912d09b-b178-4035-b7c8-7038392e2bf2 stroke:#2c3143,stroke-width:4px;
  8["Manipulate Expression Set Object"];
  7 -->|out_rds| 8;
  08de92d8-32fe-4b47-9038-298cdd13fac5["Output\nManipulate Expression Set Object on input dataset(s): ExpressionSet Object"];
  8 --> 08de92d8-32fe-4b47-9038-298cdd13fac5;
  style 08de92d8-32fe-4b47-9038-298cdd13fac5 stroke:#2c3143,stroke-width:4px;
  9["Manipulate Expression Set Object"];
  7 -->|out_rds| 9;

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-2-preparescref/workflows/sc_matrix.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