How do I set up POSTGAP?

Installing

Add the lib/ directory to your $PYTHONPATH environment variable.

Installing dependencies

To install all dependencies run sh install_dependencies.sh

Add the bin directory to your $PATH environment variable.

Flatfile preparation

• Via the FTP site (recommended)

  The following script downloads a bunch of files into PWD. sh download.sh

  Ideally, save these files in a separate directory, which we will call ```databases_dir````

  Everytime you run POSTGAP, add --database_dir /path/to/databases_dir to the command line.

• Manually (sloooow) This script will create a databases_dir directory for you:

  1. Type make download to download public databases.
  2. Type make process to preprocess the databases. Warning this may take days as it needs to split the entire 1000 Genomes files by population.