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Setup guide

Clone this project

Select a local directory and clone the main repository. Note that the Data directory will be on the same level as this repository.

git clone https://github.com/icbi-lab/mio/

Prerequisites

MIO supports python3 only and is developed and tested on 3.6 and 3.7. miopy python library is needed to run all the analysis from MIO. You will also need to have Docker and 'docker-compose' installed to run all the modules.

Required pyhton packages

To install/check python packages, in ./web run pip3 install -r requirements.txt
Note that you will need to have pip3 installed

Config local setting file

Copy and modify the setting file for the webportal which is located under ./web/mirweb/settings.py.

Few things need to be modified in the new setting file.

  • Add the desired domain or ip address to the ALLOWED_HOST list
    eg. set ALLOWED_HOST = ["*"] to allow all possible addresses

Migrate database

From ./web/ directory, run python3 manage.py makemigrations then python3 manage.py migrate

Start the webserver

From python3 manage.py runserver will bind to all address and the default TCP port 8080.
Check the website in the following link: 'http://127.0.0.1:8000/'

Create a superuser

In order to create a superuser run python3 web/manage.py createsuperuser and fill the different values.

Populate the database

The tables in txt format to populate the database are in ./Tables. We allow the user to directly copy this data in the database following the link /create_gene inside the webportal.

Activate django-rq

All the analysis are handle with django-rq. Django-rq need redis to share the information between the queues. To activate the queue run: python3 web/manage.py rqworker default slow normal faster

Create docker

To create directly the docker container with the nginx, gunicorn, django-rq, and the mio webtool the user only need to run the script run-docker.sh sudo sh scripts/run-docker.sh. The link for the webtool will be https.//localhost:8889, and the super-user: user.