Installation¶

Stable release¶

To install DEPy and all its dependencies, please clone the DEPy conda environment:

conda env create -f environment.yml
conda activate depy

This is the intended method of installation. You can install the 'summarizedpy' package on its own using pip, but please don't.

pip¶

pip install summarizedpy

Note that the SummarizedPy package must be run within the 'depy' conda environment or one cloned from it.

In short, this is because summarizedpy runs R as a subprocess in a highly defined environment to isolate it from the user's global R environment. This is necessary to ensure that Bioconductor packages load properly.