Mendel,MD

An online tool for organizing, annotating, filtering and diagnosing patients with Mendelian Disorders using Exome and Genome sequencing data.

Requirements

  • Python 3.4+
  • Perl 5.8+
  • Java 1.8
  • Ubuntu LTS 16.04

Other Libraries Needed

OMIM Data

You need to register an account at OMIM: http://omim.org/downloads and submit a download request to get a file named “morbidmap”.

After obtaining this file you need to put it inside this folder: “mendelmd_source/data/omim/”.

Docker

Now it’s possible to install and run Mendel,MD with a single command:

docker-compose up

This command will create a container, download all the required tools, datasets and run the webserver.

This should take a few hours to complete for the first time.

Manual Installation

Installing PostgreSQL Database

sudo apt-get install libpq-dev postgresql
sudo -i -u postgres
createuser --interactive
exit
createdb mendelmd
cp mendelmd/local_settings.sample.py mendelmd/local_settings.py

Installation on Ubuntu 16.04 LTS (tested)

sudo apt-get install gcc git python3-dev virtualenvwrapper zip zlibc zlib1g zlib1g-dev build-essential \
libssl-dev libffi-dev python-dev python3-dev python3-venv libcurl4-openssl-dev

python3 -m venv mendelmdenv
source mendelmdenv/bin/activate

git clone https://github.com/raonyguimaraes/mendelmd.git
cd mendelmd/mendelmd_source

Installing Pynnotator

pip install wheel
pip install pynnotator
pynnotator install

This will take a long time since it will download around 32GB of data. Go grab a coffee and read a paper.

Installing Mendel,MD

pip install -r requirements.txt

python manage.py migrate

wget https://data.omim.org/downloads/ADDYOURKEY/morbidmap.txt -O data/omim/morbidmap.txt
python manage.py populate

#create yourself a super user
python manage.py createsuperuser

python manage.py runserver

And now you should have Mendel,MD running on address http://127.0.0.1:8000/

Start the annotation

In another tab start the annotation process.

source mendelmdenv/bin/activate
celery -A mendelmd worker -l info -c 1

Creating a superuser

python manage.py createsuperuser

Importing Genes and Diseases Data

python manage.py populate

Upload your VCFs using the web interface

At the dashboard click on the “Upload VCF” button.

Deployment on RedHat/CentOS 7

https://www.digitalocean.com/community/tutorials/how-to-serve-django-applications-with-apache-and-mod_wsgi-on-centos-7

sudo yum -y install wget
wget https://data.omim.org/downloads/ADDYOURKEY/morbidmap.txt -O /tmp/morbidmap.txt
wget https://raw.github.com/raonyguimaraes/mendelmd/master/scripts/deployment_centos7_redhat7.sh
bash deployment_centos7_redhat7.sh