The code in Biostar Recipes requires Python 3.6 or above.

Our installation instructions rely on conda though other alternatives for managing python environments are equally viable.

# Create a virtual environment.
conda create -y --name engine python=3.6

# Activate the python environment.
conda activate engine

# Clone the source server code and the recipe code.
git clone

# Switch to the biostar-central directory.
cd biostar-central

# Install server dependencies.
pip install -r conf/requirements.txt

The installation is now complete. All server management commands are run through make by running one or more make tasks. For example to test the recipes app run:

make recipes test

Running a Demo

To run the demonstration version of the recipes app execute:

make recipes demo

Visit to view the site.

Initialize Recipes

Activate the engine virtual enviorment.

conda activate engine

Migrate the recipes app by executing the command:

python migrate --settings

Collect static files for the recipes app by executing the command:

python collectstatic --noinput -v 0 --settings

There is a Makefile command that migrates and collects static files in one shot.

make recipes init  # Migrate and collect static files. 

A database has now been created and the static files can be found in biostar-central/export/static/

To ensure installation and migration was successful, run a test by executing the command:

make recipes test  # Run tests. 

To populate the database with random data run:

make recipes startup

Start Server

Activate the engine virtual enviorment:

$ conda activate engine

Start a local server:

make recipes serve    # Start local server

The site is now available at

When the site initializes the admin username and password are using the ADMINS and the ADMIN_PASSWORD settings in biostar/acccounts/

By default both the admin login name and the default admin password are set to


The Django admin can be found at

Customize Settings

DO NOT add your custom settings into the public codebase!

The proper practice is to create a separate, independent settings file, then, within that file import all default settings. Finally override the fields that you wish to customize in your settings file. For example create the then add into it:

# Import all default settings.
from import *

# Now override the settings you wish to customize.
ADMIN_PASSWORD = "foopass"

Apply this settings file with

python runserver --settings

Consult the Django documentation for details.

Directory Structure

Each project has a physical directory associated on the system located on the system.

  1. Projects directory
    • Each project has a directory with the data associated.
  2. Results directory
    • Location where the results of a recipe run are stored.
  3. Table of contents directory
    • Contains table of content files for every data.

These directories all found in the media directory found in the under MEDIA_ROOT. The general structure is:


Deploying Site

The software follows the recommended practices for developing and deploying Django web applications .

The Django documentation contains a wealth of information on the alternative ways to deploy the site on different infrastructure.

Within this setup we recommend the [uwsgi][uwsgi] based deployment.