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 ## GIS tools available in Puhti
 
-* [Ames Stereo Pipeline](https://docs.csc.fi/apps/ames-stereo.md) for processing stereo images
-* [ArcGIS Python API](https://docs.csc.fi/apps/arcgis.md) 
-* [CloudCompare](https://docs.csc.fi/apps/cloudcompare.md) for visualizing, editing and processing poing clouds
-* [FORCE](https://docs.csc.fi/apps/force.md) for mass-processing of medium-resolution satellite images
-* [GDAL](https://docs.csc.fi/apps/gdal.md) for geospatial data formats
-* **[Geoconda](https://docs.csc.fi/apps/geoconda.md)** - Python spatial analysis libraries
-* [GRASS GIS](https://docs.csc.fi/apps/grass.md) General purpose GIS software family for viewing, editing and analysing geospatial data
-* [LAStools](https://docs.csc.fi/apps/lastools.md) for LiDAR datasets
+* [Ames Stereo Pipeline](https://docs.csc.fi/apps/ames-stereo/) for processing stereo images
+* [ArcGIS Python API](https://docs.csc.fi/apps/arcgis/) 
+* [CloudCompare](https://docs.csc.fi/apps/cloudcompare/) for visualizing, editing and processing poing clouds
+* [FORCE](https://docs.csc.fi/apps/force/) for mass-processing of medium-resolution satellite images
+* [GDAL](https://docs.csc.fi/apps/gdal/) for geospatial data formats
+* **[Geoconda](https://docs.csc.fi/apps/geoconda/)** - Python spatial analysis libraries
+* [GRASS GIS](https://docs.csc.fi/apps/grass/) General purpose GIS software family for viewing, editing and analysing geospatial data
+* [LAStools](https://docs.csc.fi/apps/lastools/) for LiDAR datasets
 * [MATLAB](https://docs.csc.fi/apps/matlab/)
-* [OpenDroneMap](https://docs.csc.fi/apps/opendronemap.md) for processing aerial drone imagery
-* [Orfeo ToolBox](https://docs.csc.fi/apps/otb.md) for remote sensing applications
-* [PCL](https://docs.csc.fi/apps/pcl.md) for 2D/3D image and point cloud processing
-* [PDAL](https://docs.csc.fi/apps/pdal.md) for point cloud translations and processing
-* [QGIS](https://docs.csc.fi/apps/qgis.md) General purpose GIS software family for viewing, editing and analysing geospatial data
-* **[R for GIS](https://docs.csc.fi/apps/r-env-for-gis.md)** R spataial analysis libraries
-* [SAGA GIS](https://docs.csc.fi/apps/saga-gis.md) General purpose GIS software family for viewing, editing and analysing geospatial data
-* [Sen2Cor](https://docs.csc.fi/apps/sen2cor.md) for atmospheric-, terrain and cirrus correction of the Sentinel-2 products
-* [Sen2mosaic](https://docs.csc.fi/apps/sen2mosaic.md) for download, preprocessing and mosaicing of Sentinel-2 products
-* **[SNAP](https://docs.csc.fi/apps/snap.md)** for remote sensing applications
-* [WhiteboxTools](https://docs.csc.fi/apps/whiteboxtools.md) an advanced geospatial data analysis platform
-* [Zonation](https://docs.csc.fi/apps/zonation.md) Spatial conservation prioritization framework
-* **[pytorch](https://docs.csc.fi/apps/pytorch.md)** for deep learning
-* **[tensorflow](https://docs.csc.fi/apps/tensorflow.md)** for deep learning 
+* [OpenDroneMap](https://docs.csc.fi/apps/opendronemap/) for processing aerial drone imagery
+* [Orfeo ToolBox](https://docs.csc.fi/apps/otb/) for remote sensing applications
+* [PCL](https://docs.csc.fi/apps/pcl/) for 2D/3D image and point cloud processing
+* [PDAL](https://docs.csc.fi/apps/pdal/) for point cloud translations and processing
+* [QGIS](https://docs.csc.fi/apps/qgis/) General purpose GIS software family for viewing, editing and analysing geospatial data
+* **[R for GIS](https://docs.csc.fi/apps/r-env-for-gis/)** R spataial analysis libraries
+* [SAGA GIS](https://docs.csc.fi/apps/saga-gis/) General purpose GIS software family for viewing, editing and analysing geospatial data
+* [Sen2Cor](https://docs.csc.fi/apps/sen2cor/) for atmospheric-, terrain and cirrus correction of the Sentinel-2 products
+* [Sen2mosaic](https://docs.csc.fi/apps/sen2mosaic/) for download, preprocessing and mosaicing of Sentinel-2 products
+* **[SNAP](https://docs.csc.fi/apps/snap/)** for remote sensing applications
+* [WhiteboxTools](https://docs.csc.fi/apps/whiteboxtools/) an advanced geospatial data analysis platform
+* [Zonation](https://docs.csc.fi/apps/zonation/) Spatial conservation prioritization framework
+* **[pytorch](https://docs.csc.fi/apps/pytorch/)** for deep learning
+* **[tensorflow](https://docs.csc.fi/apps/tensorflow/)** for deep learning 
 
 
 ## GIS tools available in Mahti
 
-* [Geoconda](https://docs.csc.fi/apps/geoconda.md) - Python spatial analysis libraries
-* [pytorch](https://docs.csc.fi/apps/pytorch.md) for deep learning
-* [tensorflow](https://docs.csc.fi/apps/tensorflow.md) for deep learning 
+* [Geoconda](https://docs.csc.fi/apps/geoconda/) - Python spatial analysis libraries
+* [pytorch](https://docs.csc.fi/apps/pytorch/) for deep learning
+* [tensorflow](https://docs.csc.fi/apps/tensorflow/) for deep learning 
 
 ## GIS tools available in LUMI
 
-* [GDAL](https://docs.csc.fi/apps/gdal.md) for geospatial data formats
-* [GRASS GIS](https://docs.csc.fi/apps/grass.md) General purpose GIS software family for viewing, editing and analysing geospatial data
-* [PDAL](https://docs.csc.fi/apps/pdal.md) for point cloud translations and processing
-* [QGIS](https://docs.csc.fi/apps/qgis.md) General purpose GIS software family for viewing, editing and analysing geospatial data
-* [SAGA GIS](https://docs.csc.fi/apps/saga-gis.md) General purpose GIS software family for viewing, editing and analysing geospatial data
-* [pytorch](https://docs.csc.fi/apps/pytorch.md) for deep learning
-* [tensorflow](https://docs.csc.fi/apps/tensorflow.md) for deep learning
+* [GDAL](https://docs.csc.fi/apps/gdal/) for geospatial data formats
+* [GRASS GIS](https://docs.csc.fi/apps/grass/) General purpose GIS software family for viewing, editing and analysing geospatial data
+* [PDAL](https://docs.csc.fi/apps/pdal/) for point cloud translations and processing
+* [QGIS](https://docs.csc.fi/apps/qgis/) General purpose GIS software family for viewing, editing and analysing geospatial data
+* [SAGA GIS](https://docs.csc.fi/apps/saga-gis/) General purpose GIS software family for viewing, editing and analysing geospatial data
+* [pytorch](https://docs.csc.fi/apps/pytorch/) for deep learning
+* [tensorflow](https://docs.csc.fi/apps/tensorflow/) for deep learning
 * Additional, easy to install yourself [EasyBuild recepies](https://lumi-supercomputer.github.io/LUMI-EasyBuild-docs) for CGAL, GDAL, GEOS, ncview, PROJ, R.