Ocean's variables 2.0

Run Workflow in Galaxy

• Galaxy France
• Galaxy Australia
• Galaxy Main
• Galaxy Europe
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Parameter\nWorflow fully interactive"];
  style 0 fill:#ded,stroke:#393,stroke-width:4px;
  1["ℹ️ Input Dataset\nEutrophication_Med_profiles_2022_unrestricted_SNAPSHOT_2023-10-24T16-39-44.zip"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Parameter\nWorkflow semi automatic"];
  style 2 fill:#ded,stroke:#393,stroke-width:4px;
  3["ℹ️ Input Dataset\ngebco_30sec_8.nc"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Ocean Data View"];
  1 -->|output| 4;
  5["Interactive DIVAnd jupyterlab"];
  4 -->|outputs_netcdf| 5;
  0 -->|output| 5;
  6["DIVAnd create a climatology"];
  3 -->|output| 6;
  4 -->|outputs_netcdf| 6;
  2 -->|output| 6;
  59963282-87bf-4432-a777-8a9b61dea03c["Output\nWater_body_Phosphate_Mediterranean.nc"];
  6 --> 59963282-87bf-4432-a777-8a9b61dea03c;
  style 59963282-87bf-4432-a777-8a9b61dea03c stroke:#2c3143,stroke-width:4px;
  7["ODV visualisation interactive"];
  5 -->|output_netcdf| 7;
  dc8316a4-e57c-476b-b885-bbe4fb84d8c7["Output\nOcean variables visualisation interactive"];
  7 --> dc8316a4-e57c-476b-b885-bbe4fb84d8c7;
  style dc8316a4-e57c-476b-b885-bbe4fb84d8c7 stroke:#2c3143,stroke-width:4px;
  8["ODV visualisation"];
  6 -->|output_netcdf| 8;
  7b072253-5bf9-434f-b06a-70b375ddaa03["Output\nOcean variables visualisation"];
  8 --> 7b072253-5bf9-434f-b06a-70b375ddaa03;
  style 7b072253-5bf9-434f-b06a-70b375ddaa03 stroke:#2c3143,stroke-width:4px;

Inputs

Outputs

Tools

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

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 galaxy-upload 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:

Version History

For Admins

Installing the workflow tools

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