python packages permission denied

[deniskristak]

Hello,
as part of the Easybuild project I am in need to build this software, specifically cctbx-base from source.
I am prepared to take care of all dependencies myself. The command I'm trying to run is:

python bootstrap.py --with-python $EBROOTPYTHON/bin/python --builder=cctbx --nproc %(parallel)s -v --build-dir %(builddir)s --skip-base-packages 1

However, the installer seems to ignore the argument to skip base-packages and continues to use the script install_base_packages.py anyway, which leads to an error:

Error: You don't appear to have write access to
the Python site-packages directory:
  b'/apps/gent/RHEL8/haswell-ib/software/Python/3.9.6-GCCcore-11.2.0/lib/python3.9/site-packages'
Installation of Python packages may fail.```

I suppose that the script is trying to install stuff to my python installation directly? How can I avoid it? I want it to build stuff into build-dir, which I could copy where I need it afterwards. This is because I want to build it as standalone module and not part of the Python installation directly.

Thanks!

[bkpoon]

By default, the bootstrap.py script will also try to build dependencies. You can add the hot update build commands after bootstrap.py in your command. Also, if you have all your dependencies in a $EBROOTPYTHON, you can use the --use-conda $EBROOTPYTHON to tell the build to find dependencies in $EBROOTPYTHON (essentially, adds $EBROOTPYTHON/include for headers and $EBROOTPYTHON/lib for libraries). The --use-conda flag was for building using dependencies from conda, but it is not too specific to a conda environment.