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
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()