Running GDAL processing tools from QGIS in conda environment

Question

I am trying to run Polygonize (Raster to Vector) from QGIS 3.18.3-Zürich inside a conda environment. When running the command, I encountered the following error.

Process gdal_polygonize.bat failed to start. Either gdal_polygonize.bat is missing, or you may have insufficient permissions to run the program.

I am able to load gdal from Python

(geoenv) C:\Users\jaina>python
Python 3.8.12 (default, Oct 12 2021, 03:01:40) [MSC v.1916 64 bit (AMD64)] :: Anaconda, Inc. on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> from osgeo import gdal
>>>

Also, gdalinfo works fine. I tried adding gdal scripts directory to the PATH

C:\Users\jaina\.conda\envs\geoenv\Scripts

I also tried this answer to modify system settings in QGIS but it resulted in no module SIP error on starting QGIS and processing tool bar disappears.

/Library/Frameworks/GDAL.framework/Programs:/Library/Frameworks/Python.framework/Versions/3.18.3/bin:

A similar question is unanswered here

EDIT:

Path to gdal_polygonize.bat

C:\Users\jaina\.conda\envs\geoenv>dir /s gdal_polygonize.bat
 Volume in drive C is Windows
 Volume Serial Number is 60CD-213A
File Not Found

Path to gdal_polygonize.py

C:\Users\jaina\.conda\envs\geoenv>dir /s gdal_polygonize.py

 Directory of C:\Users\jaina\.conda\envs\geoenv\Lib\site-packages\GDAL-3.3.2-py3.8-win-amd64.egg-info\scripts

16-10-2021  15:38               330 gdal_polygonize.py

 Directory of C:\Users\jaina\.conda\envs\geoenv\Lib\site-packages\osgeo_utils

01-10-2021  22:52             7,525 gdal_polygonize.py

 Directory of C:\Users\jaina\.conda\envs\geoenv\Scripts

16-10-2021  15:38               210 gdal_polygonize.py

All paths for conda environment

(geoenv) C:\Users\jaina>set PATH
Path=C:\Users\jaina\.conda\envs\geoenv;C:\Users\jaina\.conda\envs\geoenv\Library\mingw-w64\bin;C:\Users\jaina\.conda\envs\geoenv\Library\usr\bin;C:\Users\jaina\.conda\envs\geoenv\Library\bin;C:\Users\jaina\.conda\envs\geoenv\Scripts;C:\Users\jaina\.conda\envs\geoenv\bin;C:\ProgramData\Miniconda3\condabin;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\iCLS;C:\Program Files\Intel\Intel(R) Management Engine Components\iCLS;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0;C:\WINDOWS\System32\OpenSSH;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files\Git LFS;C:\Program Files\dotnet;C:\Users\jaina\.conda\envs\geoenv\Scripts;C:\Users\jaina\AppData\Local\Microsoft\WindowsApps;.
PATHEXT=.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC

Answer 1

Try to create a file $CONDA_PREFIX/bin/gdal_polygonize.bat with your text editor. In your case, it should be C:\Users\jaina\.conda\envs\geoenv\bin\gdal_polygonize.bat

Then, within the file, put the following

@echo off
%CONDA_PYTHON_EXE% "%CONDA_PREFIX%/lib/python3.8/site-packages/osgeo_utils/gdal_polygonize.py" %*

I do not know why but no .bat files were generated when installing conda. You may open an issue at https://github.com/conda-forge/qgis-feedstock/issues