https://github.com/statgen/encore
Encore Analysis Server
https://github.com/statgen/encore
Last synced: 5 months ago
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Encore Analysis Server
- Host: GitHub
- URL: https://github.com/statgen/encore
- Owner: statgen
- License: agpl-3.0
- Created: 2016-04-20T20:51:13.000Z (about 10 years ago)
- Default Branch: master
- Last Pushed: 2025-05-01T15:06:28.000Z (about 1 year ago)
- Last Synced: 2025-05-01T16:23:43.596Z (about 1 year ago)
- Language: Python
- Homepage:
- Size: 2.02 MB
- Stars: 13
- Watchers: 10
- Forks: 6
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Encore
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.
# Installing python modules
To install all the required python modules into a virtal environment
python3 -m venv venv/
source venv/bin/activate
pip install -r requirements.txt
# Run dev instance
To run a simple dev instance of Encore, you can run
./rundev.sh
# Apache Configuration
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
# Email configuration
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.
# Building Executable tools
mkdir build
cd build
cmake ..
make