Install on MacOS

MacOS Tips

Best bet is to use homebrew to install many of the binary dependencies:

brew install numpy
brew install samtools
# probably more brew install binaries that I did historically that should be mentioned here

Some tricks, for bgzip:

brew install libomp
CPPFLAGS="-I/opt/homebrew/include" pip install bgzip

You'll also need this (or something like this with different versions in the appropriate environment.py file)

GDAL_LIBRARY_PATH="/opt/homebrew/Cellar/gdal/3.4.2_2/lib/libgdal.30.dylib"
GEOS_LIBRARY_PATH="/opt/homebrew/Cellar/geos/3.10.2/lib/libgeos_c.dylib"

We've also been trying using Conda for MacOS since it bundles binaries - see the environment.yml (though this is not guarenteed to be up to date). It is recommended MacOS only be used for development, not as a server.