Installation

Development Branch Installation

Dependencies::

libmysqlclient-dev

In a virtualenv::

pip install -r pgd/requirements.txt

Master Branch Installation

This is a manual installation guide for the Protein Geometry Database

Install dependencies

The following packages are required to run Protein Geometry Database. Either install these with your system’s package manager or from Pip (recommended). Note that system packages may not have the correct version.

• Python >= 2.5 but < 3.x (Python 3.x is not supported due to backward-compatibility issues)
• setuptools >= 0.6.28
• simplejson
• MySQL-python
• numpy
• biopython 1.57
• Python Django 1.3.x
• Python Django-registration –0.7
• Py2Cairo See instructions below for installing the correct Py2Cairo
• Selenium for running browser-based tests
• liberation fonts - yum -y install git python-devel mysql-devel libffi-devel liberation-sans-fonts

The process for installing “py2cairo” was recently reported to be:

1. Install libcairo2-dev via apt-get
2. Install simplejson via pip to virtualenv
3. Retrieve py2cairo from https://github.com/dieterv/py2cairo.git
4. Run touch ChangeLog
5. Run ./autogen.sh from that checkout
6. Run ./waf configure –prefix=foo where foo is the absolute location of the virtualenv
7. Run ./waf build
8. Run ./waf install
9. Open a python interpreter and confirm that the cairo module can be imported

Get the Code

1. Make sure you have Git installed.

2. Either download and unpack the “latest release”:, or check it out from the repository:

   git clone https://github.com/osuosl/pgd
   

Configuration

1. In the project root, you’ll find a default-settings file called settings.py.dist. Copy it to settings.py:

   cp settings.py.dist settings.py
   

2. If you want to use another database engine besides the default SQLite (not recommended for production), edit settings.py, and edit the following lines to reflect your wishes:

   1 DATABASE_ENGINE = ''   # <-- Change this to 'mysql'
   2 DATABASE_NAME = ''     # <-- Change this to a database name, or a file for SQLite
   3 DATABASE_USER = ''     # <-- Change this (not needed for SQLite)
   4 DATABASE_PASSWORD = '' # <-- Change this (not needed for SQLite)
   5 DATABASE_HOST = ''     # <-- Change this (not needed if database is localhost)
   6 DATABASE_PORT = ''     # <-- Change this (not needed if database is localhost)
   

3. Initialize Database:

   ./manage.py syncdb
   

4. Everything should be all set up! Run the development server with:

   ./manage.py runserver
   

Importing Data

See the importing data section for instructions on how to import data.

Additional configuration for production servers:

Deploying a production server requires additional setup steps.

1. Change your SECRET_KEY to unique (and hopefully unguessable) strings in your settings.py.

2. Ensure the server has the ability to send emails or you have access to an SMTP server. Set EMAIL_HOST, EMAIL_PORT, and DEFAULT_FROM_EMAIL in settings.py. For more complicated outgoing mail setups, please refer to the django email documentation.

3. Follow the django guide to deploy with apache. Here is an example mod_wsgi file:

   1  import os
   2  import sys
   3
   4  path = '/var/lib/django/pgd'
   5  if path not in sys.path:
   6      sys.path.append(path)
   7
   8  os.environ['DJANGO_SETTINGS_MODULE'] = 'settings'
   9
   10 import django.core.handlers.wsgi
   11 application = django.core.handlers.wsgi.WSGIHandler()
   

4. If New Relic support is required, modify the WSGI file according to the New Relic documentation. On zeus, the New Relic configuration file is /etc/newrelic.ini.