Installation

Overview

This document will cover the installation process for this pipeline. Note that this in particular is a work in progress that will be finalized by 05 February 2021, but until then should be considered incomplete and not necessarily suitable for use.

The pipeline is configured for installation with conda. Other installation methods are possible but not supported.

Short Version (for experts)

• Install or activate conda

• If needed, install git

• Clone the analysis pipeline repository

• Navigate into the repository directory

• Create the conda environment specified by environment.yaml

• Activate the environment (make sure to do this whenever launching runs)

• Update Makefile.config to point to your copies of the following:

  • PLCO chip freeze

  • PLCO imputed data freeze

  • PLCO phenotype data

• You are now ready to start running the pipeline, good luck!

Long Version (for interested parties)

TODO