gpu_jupytool

statistics-gpu_jupyter_lab/gpu-jupyterlab-as-jupytool

Author(s)

Version
1
Last updated
Jan 18, 2023
License
None Specified, defaults to CC-BY-4.0
Tags

Features
Tutorial
A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00225
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nIPynb notebook"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["train_rows"];
  2["ℹ️ Input Dataset\ntest_rows"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\ntest_rows_labels"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["GPU enabled Interactive Jupyter Notebook for Machine Learning"];
  0 -->|output| 4;
  1 -->|out_file1| 4;
  2 -->|output| 4;
  3 -->|output| 4;
  5["Cut"];
  4 -->|output_collection| 5;

Inputs

Input Label
Input dataset IPynb notebook
Input dataset test_rows
Input dataset test_rows_labels

Outputs

From Output Label
Filter1 Filter train_rows
interactive_tool_ml_jupyter_notebook GPU enabled Interactive Jupyter Notebook for Machine Learning
Cut1 Cut

Tools

Tool Links
Cut1
Filter1
interactive_tool_ml_jupyter_notebook

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 a13a2df4e 2023-01-13 12:25:16 add get data section

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/statistics/tutorials/gpu_jupyter_lab/workflows/gpu_jupyterlab_as_jupytool.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