GTN 'Pangeo 101 for everyone - Xarray'
climate-pangeo/main-workflow
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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;
Inputs
Input | Label |
---|---|
Input parameter | plot first time e.g. index=0 |
Input dataset | CAMS-PM2_5-20211222.netcdf |
Input parameter | plot forecast time 2 days 12:00 UTC |
Input parameter | time=5 |
Input parameter | time=6 |
Input parameter | time=3 |
Input parameter | time=2 |
Input parameter | time=7 |
Input parameter | time=1 |
Input parameter | time=4 |
Input parameter | time=0 |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/0.18.2+galaxy0 | NetCDF xarray Coordinate Info | |
__EXTRACT_DATASET__ | Extract dataset | extract longitude |
__EXTRACT_DATASET__ | Extract dataset | extract latitude |
__EXTRACT_DATASET__ | Extract dataset | Extract time from coordinate info |
toolshed.g2.bx.psu.edu/repos/ecology/xarray_netcdf2netcdf/xarray_netcdf2netcdf/0.18.2+galaxy0 | NetCDF xarray operations | |
toolshed.g2.bx.psu.edu/repos/ecology/xarray_netcdf2netcdf/xarray_netcdf2netcdf/0.18.2+galaxy0 | NetCDF xarray operations | |
toolshed.g2.bx.psu.edu/repos/ecology/xarray_netcdf2netcdf/xarray_netcdf2netcdf/0.18.2+galaxy0 | NetCDF xarray operations | |
toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0 | NetCDF xarray map plotting | PM2.5 CAMS Europe 0 days 00:00 UTC (reference time) |
toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0 | NetCDF xarray map plotting | PM2.5 CAMS forecast 2 days 12:00 UTC |
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy2 | Scatterplot with ggplot2 | PM2.5 over Naples (4 days forecast) |
__EXTRACT_DATASET__ | Extract dataset | Extract times from coordinates |
__EXTRACT_DATASET__ | Extract dataset | Extract time |
toolshed.g2.bx.psu.edu/repos/climate/climate_stripes/climate_stripes/1.0.1 | climate stripes | stripes PM2.5 over Naples (4 days forecast) |
toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0 | NetCDF xarray map plotting | |
toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_montage/graphicsmagick_image_montage/1.3.31+galaxy1 | Image Montage | PM2.5 forecast 10:00 - 17:00 UTC > 30 um/m3 |
toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_montage/graphicsmagick_image_montage/1.3.31+galaxy1 | Image Montage | PM2.5 forecast 10:00 - 17:00 UTC |
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
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:
Video: Importing a workflow from URL
Version History
Version | Commit | Time | Comments |
---|---|---|---|
2 | bf3253c16 | 2021-12-28 19:46:28 | Add Galaxy workflow for Pangeo tutorial |
1 | 5851fc468 | 2021-12-23 09:04:41 | template for Galaxy Pangeo Tutorial |
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