Deploy

Getting started

Thanks to the modular structure of its design Biostar is able to integrate with a wide variety of backends and provides a number of configuration scripts and helper methods to different deployment options.

The choices made when deploying Biostar depend on the expected levels of traffic and number of posts that the site needs to manage. The examples that we provide are the two extremes, some deployments may use a combination of settings from both.

Example files can be found in the live folder named deploy.env and deploy.py.

The basic rule is to create a settings file based on the default settings. This means that the customized settings file will start with::

from biostar.settings.base import *

Then subsequently override the various settings for the current deployment. For example::

from biostar.settings.base import *
SITE_DOMAIN = "mysite.com"
SERVER_EMAIL = "myemail@mysite.com"

etc.

Technically a django deployment needs only a settings file, but in practice we use an environment file to populate a shell environment and a settings file that pulls some of these variables out of the environment.

We recommend that you start with the files in live/deploy* and copy them another name. The deploy.env and deploy.py files show the minimally necessary variables that need to be set.

source live/deploy.env
./biostar.sh test

The deploy.env must specify the correct django settings module in this case live.deploy that will load the live/deploy.py python module.

To run periodic scripts make sure that they load up the enviroment variables before executing the script.

Low traffic deployment

Suited to websites that distribute information to smaller organizations. It can be achieved with just python based solutions. Install the dependencies with::

pip install -r conf/requirements/deploy.txt

Copy the live/deploy.env and live/deploy.py files to a different name/location. For example simple.env and simple.py. Customize these as needed. To run the site invoke the waitress server that was installed above::

source live/simple.env
waitress-serve --port 8080 live.deploy.simple_wsgi:application

Create a crontab entry that updates the index every 30 minutes::

source live/simple.env
biostar.sh update_index

You are done.

High traffic deployment

While not required to be turned on the site supports compressing and precompiling the site assets. To make use of this functionality you will need to have lessc to be installed and you will need to set the USE_COMPRESSOR=True in your settings file.

To deploy the site with postgresql and elasticsearch install the requirements::

pip install --upgrade -r conf/requirements/deploy.txt

Start with the conf/defaults.env and files unde conf/deploy/* and customize them. We typically copy these into the live folder. Rember to add an __init__.py file in this folder if you want to import your settings from it.

For high performance installation we recommend deploying the production servers with the following stack:

• Front end webserver with nginx
• Biostar WSGI running via gunicorn
• Postgresql as the database
• Redis as the job queue
• Celery for running the asynchronous jobs
• Supervisord keeping everything running
• Elasticsearch as the search engine

The conf/server folder has configuration files for nginx, gunicorn and supervisord. The conf/fabs folder has Fabric files to automate a large number of site deployment operations.