Installing pip packages within conda environments on the CSF

Installing Python packages via pip within a conda environment on the CSF:

1. Load Anaconda (e.g. module load apps/anaconda3/5.2.0/bin)
2. Activate the conda environment: source activate /path/to/conda/env
3. Tell conda to exclude system-wide packages: echo "include-system-site-packages=false" >> $CONDA_PREFIX/pyvenv.cfg

4. Pass the “target” option to pip install, specifying that the package should be installed in the site packages directory of the conda environment:

   pip install --target /path/to/conda/env/lib/python_version/site-packages package-to-install

Note that we don’t need the --user option in this case (unlike when installing packages into the “root” environment on the CSF via pip).

See:

• https://stackoverflow.com/questions/51525072/global-pip-referenced-within-a-conda-environment
• https://pip.pypa.io/en/stable/reference/pip_install/#cmdoption-t