Analyse Argo data

climate-argo_pangeo/main-workflow

Author(s)
Marie Jossé
Version
1
Last updated
Mar 24, 2024
License
CC-BY-4.0
Tags
Ocean
Pangeo
earth-system

Features
Tutorial
Analyse Argo data
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00022
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["Argo data access"];
  1["NetCDF xarray Coordinate Info"];
  0 -->|output_argo| 1;
  2["NetCDF xarray Metadata Info"];
  0 -->|output_argo| 2;
  3["NetCDF timeseries Extractor"];
  0 -->|output_argo| 3;
  2 -->|output| 3;
  4["ODV"];
  3 -->|timeseries_tabular| 4;

Inputs

Input Label

Outputs

From Output Label

Tools

Tool Links
interactive_tool_odv
toolshed.g2.bx.psu.edu/repos/ecology/argo_getdata/argo_getdata/0.1.15+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ecology/timeseries_extraction/timeseries_extraction/2022.3.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/2022.3.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/2022.3.0+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
1 54b194630 2024-03-18 19:45:50 add new argo tuto

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/climate/tutorials/argo_pangeo/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