Clustering 3k PBMCs with Seurat - Workflow

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nmatrix.mtx"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\ngenes.tsv"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nbarcodes.tsv"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nCanonical Markers"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Input 3k PBMC"];
  2 -->|output| 4;
  1 -->|output| 4;
  0 -->|output| 4;
  b35bfd37-4d6b-4bdb-88af-a43b468500ca["Output\nInput 3k PBMC"];
  4 --> b35bfd37-4d6b-4bdb-88af-a43b468500ca;
  style b35bfd37-4d6b-4bdb-88af-a43b468500ca stroke:#2c3143,stroke-width:4px;
  5["Seurat Data Management"];
  4 -->|rds_out| 5;
  6["Mitochondrial Annotations"];
  4 -->|rds_out| 6;
  7["Seurat Visualize"];
  6 -->|rds_out| 7;
  8["Seurat Visualize"];
  6 -->|rds_out| 8;
  9["Seurat Visualize"];
  6 -->|rds_out| 9;
  10["Filtered Dataset"];
  6 -->|rds_out| 10;
  11["Seurat Visualize"];
  10 -->|rds_out| 11;
  12["Seurat Visualize"];
  10 -->|rds_out| 12;
  13["Seurat Visualize"];
  10 -->|rds_out| 13;
  14["Seurat Preprocessing"];
  10 -->|rds_out| 14;
  15["Seurat Preprocessing"];
  14 -->|rds_out| 15;
  16["Preprocessed Data"];
  15 -->|rds_out| 16;
  cf67e3f4-f6b2-4362-b5e3-5e9ea0aaa2a2["Output\nPreprocessed Data"];
  16 --> cf67e3f4-f6b2-4362-b5e3-5e9ea0aaa2a2;
  style cf67e3f4-f6b2-4362-b5e3-5e9ea0aaa2a2 stroke:#2c3143,stroke-width:4px;
  17["Seurat Visualize"];
  16 -->|rds_out| 17;
  18["PCA Results"];
  16 -->|rds_out| 18;
  19["Seurat Visualize"];
  18 -->|rds_out| 19;
  20["Seurat Visualize"];
  18 -->|rds_out| 20;
  21["Seurat Visualize"];
  18 -->|rds_out| 21;
  22["Seurat Visualize"];
  18 -->|rds_out| 22;
  23["Seurat Visualize"];
  18 -->|rds_out| 23;
  24["Seurat Visualize"];
  18 -->|rds_out| 24;
  25["Seurat Visualize"];
  18 -->|rds_out| 25;
  26["Seurat Find Clusters"];
  18 -->|rds_out| 26;
  27["Seurat Find Clusters"];
  26 -->|rds_out| 27;
  28["UMAP Results"];
  27 -->|rds_out| 28;
  29["Seurat Visualize"];
  28 -->|rds_out| 29;
  30["Seurat Visualize"];
  28 -->|rds_out| 30;
  31["Seurat Visualize"];
  28 -->|rds_out| 31;
  32["DE Markers"];
  28 -->|rds_out| 32;
  33["Seurat Visualize"];
  28 -->|rds_out| 33;
  34["Seurat Visualize"];
  28 -->|rds_out| 34;
  35["Seurat Visualize"];
  28 -->|rds_out| 35;
  36["Seurat Visualize"];
  28 -->|rds_out| 36;
  37["Annotated Clusters"];
  28 -->|rds_out| 37;
  4263a72f-b78f-453e-9fcb-f99d3c3633f3["Output\nAnnotated Clusters"];
  37 --> 4263a72f-b78f-453e-9fcb-f99d3c3633f3;
  style 4263a72f-b78f-453e-9fcb-f99d3c3633f3 stroke:#2c3143,stroke-width:4px;
  38["DE Markers Tabular"];
  32 -->|markers_tabular| 38;
  39["Seurat Visualize"];
  37 -->|rds_out| 39;
  40["Seurat Visualize"];
  3 -->|output| 40;
  37 -->|rds_out| 40;
  41["Input DE Markers"];
  38 -->|tabular| 41;
  2c513f2b-1f32-4ec7-bfab-afda532bc132["Output\nInput DE Markers"];
  41 --> 2c513f2b-1f32-4ec7-bfab-afda532bc132;
  style 2c513f2b-1f32-4ec7-bfab-afda532bc132 stroke:#2c3143,stroke-width:4px;
  42["Seurat Visualize"];
  41 -->|out_file1| 42;
  37 -->|rds_out| 42;

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/scrna-seurat-pbmc3k/workflows/Seurat_PBMC_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