zoechallacombe/american-gut-web

The website for the American Gut Project participant portal

american-gut-web

The website for the American Gut Project participant portal

Installation Guide for OSX

First install and run Postgres.app. Make sure that the path is configured properly so add the following to your .bash_profile:

export PATH=$PATH:/Applications/Postgres.app/Contents/Versions/9.4/bin

Now setup a new conda environment via miniconda:

conda create -n amgut python=2.7 tornado=4.4.2 psycopg2
source activate amgut

Next install and start Redis via conda.

conda install redis
redis-server

Now by forking, clone and install the repository. This will also install dependencies included in extras_require:

git clone https://github.com/YOUR-GITHUB-USERNAME/american-gut-web.git
cd american-gut-web
pip install -e .[test]

And copy over the configuration file:

cp ag_config.txt.example amgut/ag_config.txt

To configure the webserver. Feel free to fill in entries for POSTGRES and REDIS. In the existing american gut config file, the default user for POSTGRES is postgres.

To enable uuid v4 function in postgres:

echo 'CREATE EXTENSION "uuid-ossp";' | psql

Make sure that all of your permissions are set correctly. The following can be run with a user named postgres

CREATE USER postgres SUPERUSER;

See CREATE USER and ALTER USER for more details.

Finally create the database and populate it with test data, then launch the website:

./scripts/ag make test
python amgut/webserver.py

Navigating to localhost:8888 will now show the american gut site. Try using DokBF as the username to log in. All test kits have test as their password.