Inferring Trajectories with Scanpy Tutorial Workflow

single-cell-scrna-case_trajectories/inferring-trajectories-with-scanpy-workflow

Author(s)
Marisa Loach
Version
1
Last updated
Dec 8, 2023
License
CC-BY-4.0
Tags
name:singlecell

Features
Tutorial
Inferring single cell trajectories with Scanpy
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00202
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nInput Anndata"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Manipulate AnnData"];
  0 -->|output| 1;
  2["Scanpy RunFDG"];
  1 -->|anndata| 2;
  3["Scanpy PlotEmbed"];
  2 -->|output_h5ad| 3;
  4["Scanpy DiffusionMap"];
  2 -->|output_h5ad| 4;
  5["Scanpy ComputeGraph"];
  4 -->|output_h5ad| 5;
  6["Scanpy RunFDG"];
  5 -->|output_h5ad| 6;
  7["Scanpy PlotEmbed"];
  6 -->|output_h5ad| 7;
  8["Scanpy PAGA"];
  6 -->|output_h5ad| 8;
  9["Scanpy PlotTrajectory"];
  8 -->|output_h5ad| 9;
  10["Scanpy RunFDG"];
  9 -->|output_h5ad| 10;
  11["Scanpy PlotEmbed"];
  10 -->|output_h5ad| 11;
  12["Scanpy PlotEmbed"];
  10 -->|output_h5ad| 12;
  13["Scanpy PlotEmbed"];
  10 -->|output_h5ad| 13;
  14["Final Anndata with Trajectory and DPT"];
  10 -->|output_h5ad| 14;
  15["Scanpy PlotEmbed"];
  14 -->|output_h5ad| 15;

Inputs

Input Label
Input dataset Input Anndata

Outputs

From Output Label

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_trajectory/scanpy_plot_trajectory/1.8.1+galaxy9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_diffmap/scanpy_run_diffmap/1.8.1+galaxy9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_dpt/scanpy_run_dpt/1.8.1+galaxy9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_fdg/scanpy_run_fdg/1.8.1+galaxy9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_paga/scanpy_run_paga/1.8.1+galaxy9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 View in ToolShed

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

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
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 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:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
1 8968634ab 2023-09-27 14:54:04 Rename main_workflow.ga to inferring-trajectories-with-scanpy-workflow.ga

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_trajectories/workflows/inferring-trajectories-with-scanpy-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