Installing GWASpy

GWASpy leverages Hail to enable efficient processing of data directly from Google Cloud. As such, the first step is to install Hail as per instructions here. After you have installed Hail, GWASpy can be easily installed using

pip install gwaspy

It is important to note that the command above will install GWASpy locally (or wherever you ran the command). For the phasing and imputation modules using Hail Batch, this is enough. For the preimp_qc and pca modules using Hail Query, however, you have to ensure that the dataproc cluster has GWASpy, and there are examples showing how to do this in the Pre-Imputation Quality Control (QC) and Principal Component Analysis sections.