django-mips

A simple API (build on top of the Django Model API) to store and manage MIP (molecular inversion probe) markers. Detailed markers description e.g in Science 338, 1619 (2012).

package

Linux

apps for Python environment (ubuntu)

sudo apt-get install python-pip python-dev build-essential libpq-dev python-virtualenv

# optional:
sudo pip install --upgrade pip
sudo pip install --upgrade virtualenv  

download source code & go into it

git clone https://github.com/michal-stuglik/django-mips.git
# or
wget https://github.com/michal-stuglik/django-mips/archive/master.zip

install django-mips, set virtual environment & requirements

cd django-mips/

# set isolated virtual environment (VE)
virtualenv .venv

# source it
source .venv/bin/activate

# install required apps within VE
pip install -r requirements.txt

TODO: Windows

Setup & usage

outside Django project, in python scripts:

make sure you have correct database connection details in mips.dbsettings_default.py

DBNAME = ''  # database-name-on-the-host
USER = ''  # user-name
PASSWORD = ''  # set database-password
HOST = 'xxx.xxx.xxx.xxx'  # set host IP address
SECRET_KEY = 'set-secret-key-here'  # set-secret-key-here

go to project directory and load python modules from virtualenv (VE)

source .venv/bin/activate

In python

set the DJANGO_SETTINGS_MODULE environment variable to “mips.settings”

import os
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "mips.settings")

set up Django

import django
django.setup()

Examples

scripts & README

Old notes

Prerequisites

Python 2.7

Linux

probably, you already have it!

Windows

download & install: https://www.python.org/ftp/python/2.7.10/python-2.7.10.msi
remember to select "Add python.exe to Path"

pip & virtualenv (optional)

Linux (Ubuntu/Debian)

sudo apt-get install python-pip python-dev build-essential libpq-dev python-virtualenv

optional:
sudo pip install --upgrade pip
sudo pip install --upgrade virtualenv

Windows

With Python 2.7.10 version, pip is a part of the Python for Windows installer.

Windows alternatively: pip can be downloaded with this script: get-pip.py, and installed by running in console:

C:\> python get-pip.py

Requirements

Django 1.7-1.8

pip install django

Python-PostgreSQL Database Adapter

Linux

pip install psycopg2

Windows

 pip install git+https://github.com/nwcell/psycopg2-windows.git@win32-py27#egg=psycopg2

Windows alternatively: download & install from win-psycopg project site - e.g. psycopg2

 http://stickpeople.com/projects/python/win-psycopg/

Download

package

https://pypi.python.org/pypi/django-mips

source code

$ git clone https://github.com/michal-stuglik/django-mips.git
or
https://github.com/michal-stuglik/django-mips/archive/master.zip

with pip (recommended)

Install with pip (you will find mips folder in your local Python directory )

pip install django-mips

Install required modules

cd django-mips/
pip install -r requirements.txt

Upgrade

with git

cd django-mips/
git pull
pip install -r requirements.txt

with pip

pip install -django-mips --upgrade
cd django-mips/
pip install -r requirements.txt

Setup

outside Django project, in python scripts:

• set database connection details in mips.dbsettings_default.py

• set the DJANGO_SETTINGS_MODULE environment variable to “mips.settings”

  import os os.environ.setdefault("DJANGO_SETTINGS_MODULE", "mips.settings")

• set up Django: django.setup()

  import django django.setup()

Examples

scripts & README