CLM-FATES_ ALP1 simulation (5 years)

climate-fates/clm-fates-alp1-simulation-5years

Author(s)
Anne Fouilloux
Version
1
Last updated
Oct 11, 2021
License
Apache-2.0
Tags
climate

Features
Tutorial
Functionally Assembled Terrestrial Ecosystem Simulator (FATES)
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00024
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\nInput dataset for CLM-FATES"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nCLM-FATES restart file"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["CTSM/FATES-EMERALD"];
  1 -->|output| 2;
  0 -->|output| 2;
  3["Extract Dataset"];
  2 -->|history_files| 3;
  debf2e31-dbea-46d5-8644-586c9731cdbe["Output\ninput dataset(s) (extracted element)"];
  3 --> debf2e31-dbea-46d5-8644-586c9731cdbe;
  style debf2e31-dbea-46d5-8644-586c9731cdbe stroke:#2c3143,stroke-width:4px;
  4["NetCDF xarray Metadata Info"];
  3 -->|output| 4;
  5["NetCDF xarray Selection"];
  3 -->|output| 5;
  4 -->|output| 5;
  6["Replace"];
  5 -->|simpleoutput| 6;
  7["Scatterplot with ggplot2"];
  6 -->|outfile| 7;

Inputs

Input Label
Input dataset Input dataset for CLM-FATES
Input dataset CLM-FATES restart file

Outputs

From Output Label
Input dataset Input dataset for CLM-FATES
Input dataset CLM-FATES restart file
toolshed.g2.bx.psu.edu/repos/climate/ctsm_fates/ctsm_fates/2.0.1 CTSM/FATES-EMERALD
__EXTRACT_DATASET__ Extract Dataset
toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1 NetCDF xarray Metadata Info
toolshed.g2.bx.psu.edu/repos/ecology/xarray_select/xarray_select/0.15.1 NetCDF xarray Selection
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3 Replace
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy2 Scatterplot with ggplot2

Tools

Tool Links
__EXTRACT_DATASET__
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/climate/ctsm_fates/ctsm_fates/2.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ecology/xarray_select/xarray_select/0.15.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy2 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
3 ad6ca44b0 2021-10-11 11:40:01 fix wf
2 3693396f6 2021-10-05 09:44:29 add license, creator information
1 969fae434 2021-10-05 09:41:36 Add climate workflows from @annefou

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/climate/tutorials/fates/workflows/CLM-FATES_ALP1_simulation_5years.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