Encore allows scientists to test hypotheses using large scale sequencing data while hiding many of the complicated technical issues associated with working on terabyte scale data. In addition to performing the most common association tests for single variants and groups of rare variants, Encore enables users to annotate, share and interact with results. Access to Encore is controlled by a white list of users who can upload phenotypes and request analyses. All per-variant and per-gene summary statistics are returned. To maintain confidentiality of research participant data, individual level data cannot be downloaded. By optimizing the most common analyses and providing rich ways to interact with results, Encore offers an exciting platform to investigate genetic hypotheses.
Note: This page contains developer information for setting up and deploying a new instance of Encore. If you are looking for documentation on how to prepare and submit GWAS analyses using an established version of Encore, please see the Wiki.
To install all the required python modules into a virtal environment
python3 -m venv venv/
source venv/bin/activate
pip install -r requirements.txt
To run a simple dev instance of Encore, you can run
./rundev.sh
Currently Encore is deployed using WSGI with apache. You can install apache and the WSGI module with
apt-get install apache2 python-setuptools libapache2-mod-wsgi-py3 python3-dev libmysqlclient-dev
A sample wsgi file is included at encore.wsgi.example. You should copy this file to encore.wsgi and fill in the correct path for your server.
A sample apache conf file is included at encore.conf.example. You should copy this file to /etc/apache2/sites-available/encore.conf and fill in the correct URL and path for your server.
You can enable the configuration with
sudo a2ensite encore
sudo systemctl restart apache2
Encore will try to send email via localhost. You can set up postfix to send or redirect these emails how you like. You can install postfix with
sudo apt-get install postfix
A simple installation would just choose "Internet Site" and set
inet_interfaces = localhost
in the /etc/postfix/main.cf config file.
mkdir build
cd build
cmake ..
make