Hg19 Example

Purpose

This project is an example of how you can analyze and visualize a DNA data set using python, django, postgresql and postBIS.

Install requirements

If you are using a Debian based distribution:

sudo apt-get install python-dev python-setuptools git-core build-essential libdbd-pg-perl ssl-cert bedtools postgresql libpq-dev -y

Install pip

sudo easy_install pip

Install virtualenvwrapper with pip

sudo pip install virtualenvwrapper

Select a directory where you want to install all you python packages. Lets say ~/hg19/var/local/virtualenvs.

mkdir -p ~/hg19/var/local/virtualenvs

Append the following lines to ~/.bashrc

export WORKON_HOME=~/hg19/var/local/virtualenvs
source /usr/local/bin/virtualenvwrapper.sh

Clone the project

Select your working directory. Lets say ~/hg19 and call it {hg19}

cd {hg19}

git clone https://github.com/mexiCoders/hg19_example.git

Create a python virtual enviroment

mkvirtualenv hg19

workon hg19

Install project requirements

cd hg19

add2virtualenv .

workon hg19

pip install -r requirements.txt

Install postBIS

svn co https://colab.mpi-bremen.de/postbis/svn/trunk postbis

make

make install

Create the postgresql database

createdb hg19

psql hg19

In postgresql shell

CREATE EXTENSION postbis;

Download/Load data

workon hg19

cd scripts

Warning: it takes a long time

./download_and_load_chromosomes.sh

If you want to upload only a chromosome you can do this:

./download_and_load_chromosomes.sh {chromosome}