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¶
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