AnnData to Seurat conversion

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nAnnData"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Inspect AnnData"];
  0 -->|output| 1;
  6d03d713-8d71-4f6a-9f83-cd999f423ebf["Output\nInspect AnnData: obs"];
  1 --> 6d03d713-8d71-4f6a-9f83-cd999f423ebf;
  style 6d03d713-8d71-4f6a-9f83-cd999f423ebf stroke:#2c3143,stroke-width:4px;
  2["Inspect AnnData"];
  0 -->|output| 2;
  ea025a8a-6f3a-4e38-a3af-db406886c7de["Output\nInspect AnnData: X"];
  2 --> ea025a8a-6f3a-4e38-a3af-db406886c7de;
  style ea025a8a-6f3a-4e38-a3af-db406886c7de stroke:#2c3143,stroke-width:4px;
  3["Transpose"];
  2 -->|X| 3;
  4["DropletUtils"];
  3 -->|out_file| 4;
  5["Seurat Read10x"];
  4 -->|barcodes_out| 5;
  4 -->|genes_out| 5;
  4 -->|matrix_out| 5;
  1 -->|obs| 5;
  e5fec5dc-4706-48e5-8326-05e70290552d["Output\nConverted Seurat object"];
  5 --> e5fec5dc-4706-48e5-8326-05e70290552d;
  style e5fec5dc-4706-48e5-8326-05e70290552d stroke:#2c3143,stroke-width:4px;

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/scrna-data-ingest/workflows/AnnData-to-Seurat-conversion.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