BioCloud

The ultimate Django server to run NGS analysis pipeline.

Getting Started

Requirements

• Git
• Python 3.5+

Set up a Python Virtual Environment

Built-in venv

Create the virtual environment at <repo>/venv:

python3 -m venv venv

To activate it:

. venv/bin/activate

Or on Windows, use

. venv\Scripts\activate.bat

Install Dependencies

Use pip:

pip install -r requirements.txt

Set up Local Environment Variables and Database

Settings are stored in environment variables via django-environ. The quickiest way to start is to copy local.sample.env into local.env:

cp src/biocloud/settings/local.sample.env src/biocloud/settings/local.env

Then edit the SECRET_KEY line in local.env, replacing {{ secret_key }} into any Django Secret Key value. An example:

SECRET_KEY=-@5#xz3#f)4waw+p=l^c$1!6ei8&c5u_=^%*sdu(6vy@m$*-v&

After that, just run the migration.

Go Develop

Change to the src directory:

cd src

The website uses PostgreSQL database, make sure it has been running. On OSX, PostgreSQL may not run in the background, which can be started manually by

fab start_db

Then run the database migration.

python manage.py migrate

Run the development server

python manage.py runserver

the Django-Q job cluster for executing pipeline jobs

python manage.py qcluster

and a local SMTP server so all email sending will be captured

fab start_smtp

License

Release under MIT License. A great portion of code is adapted from PyCon Taiwan 2016 website's source code under license MIT.