Workflows
These workflows are associated with Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy 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.
GTN 'Pangeo 101 for everyone - Xarray'
Anne Fouilloux
Last updated Dec 28, 2021
Launch in Tutorial Mode
License:
MIT
Tests: ❌
Results: Not yet automated
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;
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 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: