genTB website

A Django site that facilitates the contribution and analysis of fastQ and VCF files.

Installation

This website requires python 3.x plus a database with GIS functions.

Create a virtualenv and install deps:

virtualenv -p python3 pythonenv
. ./pythonenv/bin/activate
python3 -m pip install --upgrade pip
pip install -r requirements.txt

Note: PyVCF can now not be installed using newer setuptools, use pip install setuptools==58 to downgrade setuptools first.

Next, you must create a database if you are using PostgreSQL or MySQL. If you are using the default SQLite, skip this.

vim ./tb-website/settings/local.py

Change settings relating to the database location, username, and password.

Finally, it would be best to make sure GIS libraries are installed (some are only required for SQLite and MySQL). The version of libgeos may differ depending on the Ubuntu version.

sudo apt install binutils libproj-dev gdal-bin libgeos-dev libsqlite3-mod-spatialite
sudo apt install postgresql-14-postgis-3

To create a database for postgres, log into psql:

CREATE DATABASE gentb_local;
CREATE USER gentb WITH PASSWORD 'password';
ALTER ROLE gentb SET client_encoding TO 'utf8';
ALTER ROLE gentb SET default_transaction_isolation TO 'read committed';
ALTER ROLE gentb SET timezone TO 'UTC';
GRANT ALL PRIVILEGES ON DATABASE gentb_local TO gentb;
ALTER DATABASE gentb_local SET timezone TO 'UTC';

\c gentb_local
CREATE EXTENSION IF NOT EXISTS postgis;

For running tests against the database:

CREATE DATABASE test_gentb_local;
GRANT ALL PRIVILEGES ON DATABASE test_gentb_local TO gentb;
ALTER DATABASE test_gentb_local SET timezone TO 'UTC';

\c test_gentb_local
CREATE EXTENSION IF NOT EXISTS postgis;

Next, you should be able to run the migration:

python manage.py migrate

If successful, everything from here is just a standard Django website.

Start the development server:

python manage.py runserver

The database will be empty, so be sure to populate it with a user account and other information you need.

Maps Testing

To test the projection, maps and other visualisations you can quickly bring a blank database up with the following commands::

./manage migrate
./manage load_map_data
./manage loaddata drugs genelocus
./manage loaddata test-genetics test-strains
./manage load_social_data
./manage runserver

The populated data will be wrong (not real) but should allow necessary testing.

MacOS:

Comment out the spatialite_library_path in your local.py file

You will likely need to install the gdal library.

homebrew

brew install gdal

macports

macports install gdal

Finally, install the required python library.

pip install gdal