EBI SCXA to AnnData (Scanpy) or Seurat Object

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Parameter\nSC-Atlas experiment accession"];
  style 0 fill:#ded,stroke:#393,stroke-width:4px;
  1["EBI SCXA Data Retrieval"];
  0 -->|output| 1;
  2["Rename batch numbers"];
  1 -->|design_tsv| 2;
  3["Mito genes check"];
  1 -->|genes_tsv| 3;
  b0762cfd-58bd-4c39-ae41-2dca4289c541["Output\nMito genes check"];
  3 --> b0762cfd-58bd-4c39-ae41-2dca4289c541;
  style b0762cfd-58bd-4c39-ae41-2dca4289c541 stroke:#2c3143,stroke-width:4px;
  4["Rename cell metadata headers"];
  2 -->|out_file1| 4;
  5["Create AnnData"];
  1 -->|barcode_tsv| 5;
  4 -->|outfile| 5;
  1 -->|genes_tsv| 5;
  1 -->|matrix_mtx| 5;
  938cd594-61cf-4037-a58b-c09c065db505["Output\nAnnData object"];
  5 --> 938cd594-61cf-4037-a58b-c09c065db505;
  style 938cd594-61cf-4037-a58b-c09c065db505 stroke:#2c3143,stroke-width:4px;
  6["Seurat Read10x"];
  1 -->|barcode_tsv| 6;
  1 -->|genes_tsv| 6;
  1 -->|matrix_mtx| 6;
  4 -->|outfile| 6;
  c24e9d83-c175-40a2-9c36-eeb486fe323e["Output\nSeurat object"];
  6 --> c24e9d83-c175-40a2-9c36-eeb486fe323e;
  style c24e9d83-c175-40a2-9c36-eeb486fe323e stroke:#2c3143,stroke-width:4px;
  7["AnnData Operations"];
  5 -->|output_h5ad| 7;
  b47f801f-bedb-4136-a5e9-378a815a1799["Output\nMito-counted AnnData for downstream analysis"];
  7 --> b47f801f-bedb-4136-a5e9-378a815a1799;
  style b47f801f-bedb-4136-a5e9-378a815a1799 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/EBI-retrieval/workflows/EBI-SCXA-to-AnnData-(Scanpy)-or-Seurat-Object.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