Image Learner - GTEx Tissue Modeling

statistics-GTEx_Tissue_modeling/main-workflow

Author(s)
Paulo Cilas Morais Lyra Junior, Jeremy Goecks
Version
1
Last updated
Jul 24, 2026
License
AGPL-3.0-or-later
Tags
GTEx
Tissue_Classification
Gene_Expression
Image_Learner

Features
Tutorial
GTEx Tissue Modeling with Galaxy Image Learner
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00385
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\nselected_gtex_v11_tpm_image_tissue_labels.csv"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nselected_gtex_v11_tpm_image_tissue_dataset.zip"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Image Learner"];
  1 -->|output| 2;
  0 -->|output| 2;
  d593191c-7025-48f5-8946-edbb6c5defd6["Output\npredictions"];
  2 --> d593191c-7025-48f5-8946-edbb6c5defd6;
  style d593191c-7025-48f5-8946-edbb6c5defd6 stroke:#2c3143,stroke-width:4px;
  51ccf34c-95c2-4c4e-a975-4982859c291a["Output\nmodel"];
  2 --> 51ccf34c-95c2-4c4e-a975-4982859c291a;
  style 51ccf34c-95c2-4c4e-a975-4982859c291a stroke:#2c3143,stroke-width:4px;
  956b787c-8a35-41a6-b687-1a39076a1abb["Output\nreport"];
  2 --> 956b787c-8a35-41a6-b687-1a39076a1abb;
  style 956b787c-8a35-41a6-b687-1a39076a1abb stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset selected_gtex_v11_tpm_image_tissue_labels.csv
Input dataset selected_gtex_v11_tpm_image_tissue_dataset.zip

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/goeckslab/image_learner/image_learner/0.1.5 Image Learner

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/goeckslab/image_learner/image_learner/0.1.5 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
  1. Click on Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on Import at the top-right of the screen
  3. 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”
  4. 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
3 78f6f9072 2026-05-04 17:42:00 text update
2 fa9cf12cf 2026-05-03 14:07:14 update tutorial with imgs
1 dc4642c7e 2026-05-01 16:39:37 GTEx initial tutorail

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/statistics/tutorials/GTEx_Tissue_modeling/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