earth community automatic resources update

communities/earth/lab/sections/4_tutorials.yml

@@ -3,60 +3,61 @@ title: Earth-system tutorials
 tabs:
 - id: climate
   title: Climate
-  heading_md: 'Top 10 most visited tutorials for the Topic : Climate'
+  heading_md: 'Top 10 most visited tutorials for the Topic : Climate. <br/> Visitors
+    : Number of unique visitors automatically calculated using Plausible.'
   content:
-  - title_md: "Pangeo Notebook in Galaxy - Introduction to Xarray\n (Visitors: 2974553)"
+  - title_md: "Pangeo Notebook in Galaxy - Introduction to Xarray\n (Visitors: 3381481)"
     description_md: Tutorial stored in Climate topic on the Galaxy Training 
       Network and covering topics related to nan
     button_link: 
       https://training.galaxyproject.org//topics/climate/tutorials/pangeo-notebook/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
   - title_md: "Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools\n\
-      \ (Visitors: 2974279)"
+      \ (Visitors: 3381167)"
     description_md: Tutorial stored in Climate topic on the Galaxy Training 
       Network and covering topics related to nan
     button_link: 
       https://training.galaxyproject.org//topics/climate/tutorials/pangeo/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: "Ocean Data View (ODV)\n (Visitors: 503)"
+  - title_md: "Ocean Data View (ODV)\n (Visitors: 576)"
     description_md: Tutorial stored in Climate topic on the Galaxy Training 
       Network and covering topics related to nan
     button_link: 
       https://training.galaxyproject.org//topics/climate/tutorials/ocean-data-view/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: "Analyse Argo data\n (Visitors: 361)"
+  - title_md: "Sentinel 5P data visualisation\n (Visitors: 425)"
     description_md: Tutorial stored in Climate topic on the Galaxy Training 
       Network and covering topics related to nan
     button_link: 
-      https://training.galaxyproject.org//topics/climate/tutorials/argo_pangeo/tutorial.html
+      https://training.galaxyproject.org//topics/climate/tutorials/sentinel5_data/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: "Sentinel 5P data visualisation\n (Visitors: 358)"
+  - title_md: "Analyse Argo data\n (Visitors: 424)"
     description_md: Tutorial stored in Climate topic on the Galaxy Training 
       Network and covering topics related to nan
     button_link: 
-      https://training.galaxyproject.org//topics/climate/tutorials/sentinel5_data/tutorial.html
+      https://training.galaxyproject.org//topics/climate/tutorials/argo_pangeo/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: "Ocean's variables study\n (Visitors: 264)"
+  - title_md: "Ocean's variables study\n (Visitors: 308)"
     description_md: Tutorial stored in Climate topic on the Galaxy Training 
       Network and covering topics related to nan
     button_link: 
       https://training.galaxyproject.org//topics/climate/tutorials/ocean-variables/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: "Getting your hands-on earth data\n (Visitors: 159)"
+  - title_md: "Getting your hands-on earth data\n (Visitors: 212)"
     description_md: Tutorial stored in Climate topic on the Galaxy Training 
       Network and covering topics related to nan
     button_link: 
       https://training.galaxyproject.org//topics/climate/tutorials/earth_system/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
   - title_md: "Nitrate DMQC for autonomous platforms such as Argo floats\n (Visitors:
-      91)"
+      135)"
     description_md: Tutorial stored in Climate topic on the Galaxy Training 
       Network and covering topics related to nan
     button_link: 
@@ -65,49 +66,50 @@ tabs:
     button_icon: tutorial
 - id: ecology
   title: Ecology
-  heading_md: 'Top 10 most visited tutorials for the Topic : Ecology'
+  heading_md: 'Top 10 most visited tutorials for the Topic : Ecology. <br/> Visitors
+    : Number of unique visitors automatically calculated using Plausible.'
   content:
   - title_md: "Visualization of Climate Data using  NetCDF xarray Map Plotting\n (Visitors:
-      2483)"
+      2638)"
     description_md: Tutorial stored in Ecology topic on the Galaxy Training 
       Network and covering topics related to nan
     button_link: 
       https://training.galaxyproject.org//topics/ecology/tutorials/x-array-map-plot/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: "Ecoregionalization workflow tutorial\n (Visitors: 369)"
+  - title_md: "Ecoregionalization workflow tutorial\n (Visitors: 476)"
     description_md: Tutorial stored in Ecology topic on the Galaxy Training 
       Network and covering topics related to nan
     button_link: 
       https://training.galaxyproject.org//topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: "Obis marine indicators\n (Visitors: 340)"
+  - title_md: "Obis marine indicators\n (Visitors: 403)"
     description_md: Tutorial stored in Ecology topic on the Galaxy Training 
       Network and covering topics related to Biodiversity, Ecology, Data mining
     button_link: 
       https://training.galaxyproject.org//topics/ecology/tutorials/obisindicators/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: "QGIS Web Feature Services\n (Visitors: 333)"
+  - title_md: "QGIS Web Feature Services\n (Visitors: 395)"
     description_md: Tutorial stored in Ecology topic on the Galaxy Training 
       Network and covering topics related to nan
     button_link: 
       https://training.galaxyproject.org//topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: "From NDVI data with OpenEO to time series visualisation with Holoviews\n\
-      \ (Visitors: 256)"
+  - title_md: "Marine Omics identifying biosynthetic gene clusters\n (Visitors: 331)"
     description_md: Tutorial stored in Ecology topic on the Galaxy Training 
       Network and covering topics related to nan
     button_link: 
-      https://training.galaxyproject.org//topics/ecology/tutorials/ndvi_openeo/tutorial.html
+      https://training.galaxyproject.org//topics/ecology/tutorials/marine_omics_bgc/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial
-  - title_md: "Marine Omics identifying biosynthetic gene clusters\n (Visitors: 248)"
+  - title_md: "From NDVI data with OpenEO to time series visualisation with Holoviews\n\
+      \ (Visitors: 291)"
     description_md: Tutorial stored in Ecology topic on the Galaxy Training 
       Network and covering topics related to nan
     button_link: 
-      https://training.galaxyproject.org//topics/ecology/tutorials/marine_omics_bgc/tutorial.html
+      https://training.galaxyproject.org//topics/ecology/tutorials/ndvi_openeo/tutorial.html
     button_tip: View tutorial
     button_icon: tutorial

communities/earth/metadata/tool_status.tsv

@@ -24,9 +24,12 @@ data_exploration	ecology	Explore data through multiple statistical tools	True	Fa
 dose_response_analysis_tool	ufz	A  tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses	True	False
 earth	ecology	Access, process, visualise oceanographic data for the Earth System	True	False
 ecoregionalization	ecology	Tools to compute ecoregionalization with BRT model predictions and clustering.	True	False
+effective_population_size_ld_method	ecology	Tool to estimate the LDNe using NeEstimator via the RLDNe package.		
 emlassemblyline	ecology	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa	True	False
 eodie	climate	Earth Observation Data Information Extractor	True	False
 gdal	ecology	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.	True	False
+genetic_clustering	ecology	Tools for genetic population structure inference using LEA (sNMF) and DPAC (K-means).		
+genetic_format_conversion	ecology	This tool enables the conversion and formatting of genotyping data between VCF, GENEPOP, SSR (tabular) and BayeScan formats.		
 hirondelle_crim_ogc_api_processes	ecology	This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.	True	False
 interpolation	ecology	Run IDW interpolation based on a .csv and .geojson file	True	False
 marine_omics	ecology	The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data	True	False
@@ -40,6 +43,7 @@ ocean_neural_network	ecology	Robust Estimation of Open Ocean CO2 Variables and N
 ogcProcess_otb_bandmath	ecology	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.	True	False
 ogcProcess_otb_meanShiftSmoothing	ecology	This application smooths an image using the MeanShift algorithm.	True	False
 pampa	ecology	Tools to compute and analyse biodiversity metrics	True	False
+population_genetics_stats	ecology	This tool computes standard genetic diversity statistics and differentiation indices.		
 population_genomics_vcftoolbox	ecology	Tools to filter, manipulate, and manage VCF files for population genomics analyses using vcftools and bcftools.		
 psy_maps	climate	Visualization of regular geographical data on a map with psyplot	True	False
 regionalgam	ecology		True	False
@@ -49,6 +53,7 @@ sdmpredictors	ecology	Terrestrial and marine predictors for species distribution
 shift_longitudes	climate	Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees	True	False
 spocc_occ	ecology	Get species occurences data	True	False
 srs_tools	ecology	Compute biodiversity indicators for remote sensing data from Sentinel 2	True	False
+ssr_filtering	ecology	Tool to filter SSR genotype data for missing data and null alleles.		
 stoceps	ecology	Tools to analyse STOC data.	True	False
 terrabyte_ogc_api_processes	ecology	This tool is a wrapper for OGC API Processes (OTB) coming from terrabyte (https://docs.terrabyte.lrz.de/).	True	False
 vigiechiro	ecology	Tools created by the vigiechiro team to analyses and identify chiro sounds files.	True	False

communities/earth/metadata/workflow_status.tsv

@@ -2,18 +2,18 @@ Link	Name	Source	Projects	Creators	Creation time	Update time	To keep	Deprecated
 https://workflowhub.eu/workflows/758?version=1	Calculating and visualizing OBIS marine biodiversity indicators	WorkflowHub	EuroScienceGateway	Marie Josse	2024-02-15	2025-11-06	True	False
 https://workflowhub.eu/workflows/756?version=1	Sentinel 5P volcanic data visualization	WorkflowHub	EuroScienceGateway	Marie Jossé	2024-02-15	2025-11-04	True	False
 https://workflowhub.eu/workflows/1182?version=1	Ocean's variables 2.0	WorkflowHub	FAIR-EASE, usegalaxy-eu	Marie Jossé	2024-10-18	2024-10-18	True	False
-https://workflowhub.eu/workflows/1113?version=1	Full Analyse Argo data	WorkflowHub	FAIR-EASE, usegalaxy-eu	Marie Jossé	2024-09-02	2024-09-02	True	False
-https://workflowhub.eu/workflows/1105?version=1	Marine Omics identifying biosynthetic gene clusters	WorkflowHub	FAIR-EASE, usegalaxy-eu	Marie Jossé	2024-08-21	2024-08-21	True	False
-https://workflowhub.eu/workflows/252?version=1	Pangeo 101 for everyone - introduction to Xarray	WorkflowHub	Galaxy Climate		2021-12-29	2023-01-16	True	False
-https://workflowhub.eu/workflows/123?version=1	Compute daily and monthly mean from meteorological station measurements	WorkflowHub	Galaxy Climate		2021-05-23	2023-01-16	True	False
-https://workflowhub.eu/workflows/46?version=1	Copernicus Essential Climate Variable - select and plot	WorkflowHub	Galaxy Climate		2020-07-23	2023-01-16	True	False
+https://workflowhub.eu/workflows/1113?version=1	Full Analyse Argo data	WorkflowHub	FAIR-EASE, usegalaxy-eu	Marie Jossé	2024-09-02	2026-05-13	True	False
+https://workflowhub.eu/workflows/1105?version=1	Marine Omics identifying biosynthetic gene clusters	WorkflowHub	FAIR-EASE, usegalaxy-eu	Marie Jossé	2024-08-21	2026-05-13	True	False
+https://workflowhub.eu/workflows/252?version=1	Pangeo 101 for everyone - introduction to Xarray	WorkflowHub	Galaxy Climate		2021-12-29	2026-05-13	True	False
+https://workflowhub.eu/workflows/123?version=1	Compute daily and monthly mean from meteorological station measurements	WorkflowHub	Galaxy Climate		2021-05-23	2026-05-13	True	False
+https://workflowhub.eu/workflows/46?version=1	Copernicus Essential Climate Variable - select and plot	WorkflowHub	Galaxy Climate		2020-07-23	2026-05-13	True	False
 https://workflowhub.eu/workflows/1652?version=1	Xarray_Map_Plotting_Workflow	WorkflowHub	Galaxy Training Network		2025-06-02	2025-06-02	True	False
 https://workflowhub.eu/workflows/1625?version=1	Retrieve climate data from Copernicus	WorkflowHub	Galaxy Training Network		2025-06-02	2025-06-02	True	False
 https://workflowhub.eu/workflows/1441?version=1	Climate 101	WorkflowHub	Galaxy Training Network		2025-06-02	2025-06-02	True	False
 https://workflowhub.eu/workflows/1432?version=1	GTN 'Pangeo 101 for everyone - Xarray'	WorkflowHub	Galaxy Training Network		2025-06-02	2025-06-09	True	False
 https://workflowhub.eu/workflows/1427?version=1	CLM-FATES_ ALP1 simulation (5 years)	WorkflowHub	Galaxy Training Network		2025-06-02	2025-06-02	True	False
 https://workflowhub.eu/workflows/1423?version=1	Pangeo Jupyter Notebook	WorkflowHub	Galaxy Training Network		2025-06-02	2025-06-02	True	False
-https://workflowhub.eu/workflows/42?version=1	Climate - Climate 101	WorkflowHub	Galaxy Training Network	Anne Fouilloux	2020-06-29	2023-01-16	True	False
+https://workflowhub.eu/workflows/42?version=1	Climate - Climate 101	WorkflowHub	Galaxy Training Network	Anne Fouilloux	2020-06-29	2026-05-13	True	False
 https://workflowhub.eu/workflows/1698?version=1	Marine Omics visualisation	WorkflowHub	Galaxy Training Network, EuroScienceGateway	Marie Jossé, Yvan Le Bras	2025-06-02	2025-11-04	True	False
 https://workflowhub.eu/workflows/1663?version=1	Marine Omics identifying biosynthetic gene clusters	WorkflowHub	Galaxy Training Network, EuroScienceGateway	Marie Jossé	2025-06-02	2025-07-28	True	False
 https://workflowhub.eu/workflows/1436?version=1	Analyse Argo data	WorkflowHub	Galaxy Training Network, EuroScienceGateway	Marie Jossé	2025-06-02	2025-07-28	True	False