RaceID Workflow

single-cell-scrna-raceid/raceid-workflow

Author(s)
Mehmet Tekman, Alex Ostrovsky
Version
1
Last updated
Dec 13, 2024
License
CC-BY-4.0
Tags
transcriptomics
single-cell

Features
Tutorial
Downstream Single-cell RNA analysis with RaceID
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00295
RO-Crate logo with flask Download Workflow RO-Crate
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nTabular Matrix"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Initial processing using RaceID"];
  0 -->|output| 1;
  2["Clustering using RaceID"];
  1 -->|outrdat| 2;
  3["Lineage computation using StemID"];
  2 -->|outrdat| 3;
  4["Cluster Inspection using RaceID"];
  2 -->|outrdat| 4;
  5["Cluster Inspection using RaceID"];
  2 -->|outrdat| 5;
  6["Cluster Inspection using RaceID"];
  2 -->|outrdat| 6;
  7["Lineage Branch Analysis using StemID"];
  3 -->|outrdat| 7;
  8["Lineage Branch Analysis using StemID"];
  3 -->|outrdat| 8;

Inputs

Input Label
Input dataset Tabular Matrix

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy0 Initial processing using RaceID
toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy0 Clustering using RaceID
toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy0 Lineage computation using StemID
toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy0 Cluster Inspection using RaceID
toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy0 Cluster Inspection using RaceID
toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy0 Cluster Inspection using RaceID
toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy0 Lineage Branch Analysis using StemID
toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy0 Lineage Branch Analysis using StemID

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy0 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
2 982252087 2024-12-13 15:34:50 update workflow with authors and license
1 15a43b262 2024-12-13 13:50:34 add workflow test for single-cell raceid tutorial

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-raceid/workflows/RaceID-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