For what it’s worth, I had a similar error when installing via python setup.py develop. But my “Permission denied” error was coming from the build-script running Ninja, and for some reason it was attempting to run /usr/local/bin/ninja --version rather than /home/username/conda-env/bin/ninja --version.
I couldn’t get the build-script to use the correct Ninja, but the solution that worked for me was to run  python setup.py develop --cmake instead.