GTN 'Pangeo 101 for everyone - Xarray'

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Parameter\nplot first time e.g. index=0"];
  style 0 fill:#ded,stroke:#393,stroke-width:4px;
  1["ℹ️ Input Dataset\nCAMS-PM2_5-20211222.netcdf"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Parameter\nplot forecast time 2 days 12:00 UTC"];
  style 2 fill:#ded,stroke:#393,stroke-width:4px;
  3["ℹ️ Input Parameter\ntime=5"];
  style 3 fill:#ded,stroke:#393,stroke-width:4px;
  4["ℹ️ Input Parameter\ntime=6"];
  style 4 fill:#ded,stroke:#393,stroke-width:4px;
  5["ℹ️ Input Parameter\ntime=3"];
  style 5 fill:#ded,stroke:#393,stroke-width:4px;
  6["ℹ️ Input Parameter\ntime=2"];
  style 6 fill:#ded,stroke:#393,stroke-width:4px;
  7["ℹ️ Input Parameter\ntime=7"];
  style 7 fill:#ded,stroke:#393,stroke-width:4px;
  8["ℹ️ Input Parameter\ntime=1"];
  style 8 fill:#ded,stroke:#393,stroke-width:4px;
  9["ℹ️ Input Parameter\ntime=4"];
  style 9 fill:#ded,stroke:#393,stroke-width:4px;
  10["ℹ️ Input Parameter\ntime=0"];
  style 10 fill:#ded,stroke:#393,stroke-width:4px;
  11["NetCDF xarray Coordinate Info"];
  1 -->|output| 11;
  12["NetCDF xarray Metadata Info"];
  1 -->|output| 12;
  13["extract longitude"];
  11 -->|output_dir| 13;
  14["extract latitude"];
  11 -->|output_dir| 14;
  15["Extract time from coordinate info"];
  11 -->|output_dir| 15;
  3b4968d7-8984-4e66-87a9-a3ab8fc12ca4["Output\ninput dataset(s) (extracted element)"];
  15 --> 3b4968d7-8984-4e66-87a9-a3ab8fc12ca4;
  style 3b4968d7-8984-4e66-87a9-a3ab8fc12ca4 stroke:#2c3143,stroke-width:4px;
  16["NetCDF xarray operations"];
  1 -->|output| 16;
  14 -->|output| 16;
  13 -->|output| 16;
  12 -->|output| 16;
  17["NetCDF xarray operations"];
  1 -->|output| 17;
  15 -->|output| 17;
  12 -->|output| 17;
  18["NetCDF xarray operations"];
  1 -->|output| 18;
  15 -->|output| 18;
  14 -->|output| 18;
  13 -->|output| 18;
  12 -->|output| 18;
  19["PM2.5 CAMS Europe 0 days 00:00 UTC reference time"];
  15 -->|output| 19;
  0 -->|output| 19;
  1 -->|output| 19;
  12 -->|output| 19;
  42483031-21e2-4d88-8898-4a9aa9bb10e5["Output\nPM2.5 reference date Europe"];
  19 --> 42483031-21e2-4d88-8898-4a9aa9bb10e5;
  style 42483031-21e2-4d88-8898-4a9aa9bb10e5 stroke:#2c3143,stroke-width:4px;
  20["PM2.5 CAMS forecast 2 days 12:00 UTC"];
  15 -->|output| 20;
  2 -->|output| 20;
  1 -->|output| 20;
  12 -->|output| 20;
  07ba8141-bad3-4a61-833d-3b3e82b53fdb["Output\nPM2.5 fc 2 days 12:00 UTC Europe"];
  20 --> 07ba8141-bad3-4a61-833d-3b3e82b53fdb;
  style 07ba8141-bad3-4a61-833d-3b3e82b53fdb stroke:#2c3143,stroke-width:4px;
  21["NetCDF xarray Selection"];
  16 -->|output_netcdf| 21;
  12 -->|output| 21;
  22["NetCDF xarray Coordinate Info"];
  17 -->|output_netcdf| 22;
  23["NetCDF xarray Coordinate Info"];
  18 -->|output_netcdf| 23;
  24["NetCDF xarray Metadata Info"];
  18 -->|output_netcdf| 24;
  25["Column Regex Find And Replace"];
  21 -->|simpleoutput| 25;
  26["PM2.5 over Naples 4 days forecast"];
  21 -->|simpleoutput| 26;
  8984beb4-e593-42f8-8de5-0e92631061c7["Output\n1D plot PM2.5 over Naples (4 days forecast)"];
  26 --> 8984beb4-e593-42f8-8de5-0e92631061c7;
  style 8984beb4-e593-42f8-8de5-0e92631061c7 stroke:#2c3143,stroke-width:4px;
  27["Extract times from coordinates"];
  22 -->|output_dir| 27;
  28["Extract time"];
  23 -->|output_dir| 28;
  29[" stripes PM2.5 over Naples 4 days forecast"];
  25 -->|out_file1| 29;
  92cad576-78b5-4e07-9a07-6f05ff8f4a56["Output\nPM2.5 stripes Naples for 4 days forecast from reference date"];
  29 --> 92cad576-78b5-4e07-9a07-6f05ff8f4a56;
  style 92cad576-78b5-4e07-9a07-6f05ff8f4a56 stroke:#2c3143,stroke-width:4px;
  30["NetCDF xarray map plotting"];
  27 -->|output| 30;
  0 -->|output| 30;
  18 -->|output_netcdf| 30;
  24 -->|output| 30;
  31["NetCDF xarray map plotting"];
  28 -->|output| 31;
  6 -->|output| 31;
  18 -->|output_netcdf| 31;
  24 -->|output| 31;
  32["NetCDF xarray map plotting"];
  28 -->|output| 32;
  8 -->|output| 32;
  18 -->|output_netcdf| 32;
  24 -->|output| 32;
  33["NetCDF xarray map plotting"];
  28 -->|output| 33;
  5 -->|output| 33;
  18 -->|output_netcdf| 33;
  24 -->|output| 33;
  34["NetCDF xarray map plotting"];
  28 -->|output| 34;
  9 -->|output| 34;
  18 -->|output_netcdf| 34;
  24 -->|output| 34;
  35["NetCDF xarray map plotting"];
  28 -->|output| 35;
  4 -->|output| 35;
  18 -->|output_netcdf| 35;
  24 -->|output| 35;
  36["NetCDF xarray map plotting"];
  28 -->|output| 36;
  7 -->|output| 36;
  18 -->|output_netcdf| 36;
  24 -->|output| 36;
  37["NetCDF xarray map plotting"];
  28 -->|output| 37;
  3 -->|output| 37;
  18 -->|output_netcdf| 37;
  24 -->|output| 37;
  38["NetCDF xarray map plotting"];
  28 -->|output| 38;
  3 -->|output| 38;
  18 -->|output_netcdf| 38;
  24 -->|output| 38;
  39["NetCDF xarray map plotting"];
  28 -->|output| 39;
  4 -->|output| 39;
  18 -->|output_netcdf| 39;
  24 -->|output| 39;
  40["NetCDF xarray map plotting"];
  28 -->|output| 40;
  10 -->|output| 40;
  18 -->|output_netcdf| 40;
  24 -->|output| 40;
  41["NetCDF xarray map plotting"];
  28 -->|output| 41;
  5 -->|output| 41;
  18 -->|output_netcdf| 41;
  24 -->|output| 41;
  42["NetCDF xarray map plotting"];
  28 -->|output| 42;
  6 -->|output| 42;
  18 -->|output_netcdf| 42;
  24 -->|output| 42;
  43["NetCDF xarray map plotting"];
  28 -->|output| 43;
  10 -->|output| 43;
  18 -->|output_netcdf| 43;
  24 -->|output| 43;
  44["NetCDF xarray map plotting"];
  28 -->|output| 44;
  7 -->|output| 44;
  18 -->|output_netcdf| 44;
  24 -->|output| 44;
  45["NetCDF xarray map plotting"];
  28 -->|output| 45;
  9 -->|output| 45;
  18 -->|output_netcdf| 45;
  24 -->|output| 45;
  46["NetCDF xarray map plotting"];
  28 -->|output| 46;
  8 -->|output| 46;
  18 -->|output_netcdf| 46;
  24 -->|output| 46;
  47["Merge collections"];
  30 -->|output_dir| 47;
  32 -->|output_dir| 47;
  31 -->|output_dir| 47;
  33 -->|output_dir| 47;
  34 -->|output_dir| 47;
  37 -->|output_dir| 47;
  35 -->|output_dir| 47;
  36 -->|output_dir| 47;
  48["Merge collections"];
  43 -->|output_dir| 48;
  46 -->|output_dir| 48;
  42 -->|output_dir| 48;
  41 -->|output_dir| 48;
  45 -->|output_dir| 48;
  38 -->|output_dir| 48;
  39 -->|output_dir| 48;
  44 -->|output_dir| 48;
  49["PM2.5 forecast 10:00 - 17:00 UTC > 30 um/m3"];
  47 -->|output| 49;
  1c16eeb7-dfe1-40de-9be7-3aa2a8568308["Output\nPM2.5 (values > 30 um/m3)  fc 10:00 - 17:00 UTC over Italy"];
  49 --> 1c16eeb7-dfe1-40de-9be7-3aa2a8568308;
  style 1c16eeb7-dfe1-40de-9be7-3aa2a8568308 stroke:#2c3143,stroke-width:4px;
  50["PM2.5 forecast 10:00 - 17:00 UTC "];
  48 -->|output| 50;
  070fe227-b533-4c77-bed0-4d005b174920["Output\nPM2.5 fc 10:00 - 17:00 UTC over Italy"];
  50 --> 070fe227-b533-4c77-bed0-4d005b174920;
  style 070fe227-b533-4c77-bed0-4d005b174920 stroke:#2c3143,stroke-width:4px;

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/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