Documentation

List where everything is

• sphinx example: Lookups module (everything else needs to be adapted for docstring style etc.)

In swefreq-browser/docs:

• NOTES-shared_data.txt

  Notes that I (Andreas) wrote while implementing the facility to store multiple datasets. It is a table showing what data is shared between datasets (reference genome data) and what data is not shared. It also shows the MongoDB table names and what file (browser configuration parameter) this data is read from.

• README-VCF_requirements.txt

  This documents the expectations that we have on the VCF files that are given to us. It also tries to sort out what fields the Python loading script uses and how.

• README-loading_data.txt

  A glorified "work log" for loading data into the MongoDB database using the original Python loading scripts of ExAC, also covering how to download and prepare the various bits of reference data for loading. This document is updated for the way that we support multiple datasets in MongoDB.

In swefreq-config:

• README.md

  Documents the container setup and procedure for deployment through Ansible, etc.

In NBIS internal redmine system.

• Information about system setup is in the wiki of the old swefreq project.