CP_object_tracking_example

Run Workflow in Galaxy

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

flowchart TD
  0["Starting Modules"];
  1["ℹ️ Input Dataset\nInput dataset"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ColorToGray"];
  0 -->|output_pipeline| 2;
  3["Unzip"];
  1 -->|output| 3;
  4["IdentifyPrimaryObjects"];
  2 -->|output_pipeline| 4;
  5["MeasureObjectSizeShape"];
  4 -->|output_pipeline| 5;
  6["MeasureObjectIntensity"];
  5 -->|output_pipeline| 6;
  7["TrackObjects"];
  6 -->|output_pipeline| 7;
  8["OverlayOutlines"];
  7 -->|output_pipeline| 8;
  9["Tile"];
  8 -->|output_pipeline| 9;
  10["SaveImages"];
  9 -->|output_pipeline| 10;
  11["ExportToSpreadsheet"];
  10 -->|output_pipeline| 11;
  12["CellProfiler"];
  3 -->|unzipped| 12;
  11 -->|output_pipeline| 12;
  dab4a9ee-fb53-4c74-93f5-8a0c7f7eb13e["Output\nCellProfiler pipeline output files"];
  12 --> dab4a9ee-fb53-4c74-93f5-8a0c7f7eb13e;
  style dab4a9ee-fb53-4c74-93f5-8a0c7f7eb13e 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

• 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/imaging/tutorials/object-tracking-using-cell-profiler/workflows/main_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