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BioDesigner

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Synthetic Biology Design toolkit

Installation Guide

NOTE:

  • We're going to assume that you have installed Python 2 and MySQL 5.x and git on your computer.

####Download source code from github

git clone https://github.com/igemsoftware/HFUT-China_2015

git checkout master

Install Django

  1. Install pip

    For Unbuntu/Mint Users:

    apt-get install python-pip
    

    Or you can get standalone pip installer.

  2. Install Django using pip

    For users who has installed pip

    pip install django==1.7.6
    

    Or you can install Django manually.

    Tip: Know more information on install Django at https://docs.djangoproject.com/en/1.6/intro/install/

3.Install additional mysql & python dev lib

sudo apt-get install python-dev libmysqlclient-dev    

Set up BioDesigner

  1. Open BioDesigner/settings.py.
  2. Edit your database configuration at line 67.

Set up Database

  1. To connect MySQL in Python, we need install mysql-python first. You can install it using pip:

    pip install mysql-python
    

    Tip: If you get error message like this: EnvironmentError: mysql_config not found.

    Reference: http://stackoverflow.com/questions/7475223/mysql-config-not-found-when-installing-mysqldb-python-interface

  2. Create database named biodesigner in MySQL.

  3. Database import

	cd /path/to/the/app
	sudo mysql -e 'CREATE DATABASE biodesigner'
	python manage.py syncdb --noinput
	sudo mysql -e 'source xxx.sql' -u username --password=password biodesigner;

Install Additional Package

1.Pillow

	pip install pillow
  1. Install Elasticsearch

    For Ubuntu/Mint Users: Elasticsearch is running on Java, if you don't have a JRE on your machine, please install one.

    For example, We use OpenJDK7:

    apt-get install openjdk-7-jre
    

    Download and install the Public Signing Key

    wget -qO - http://packages.elasticsearch.org/GPG-KEY-elasticsearch | sudo apt-key add -
    

    Add the following to your /etc/apt/sources.list to enable the repository

    deb http://packages.elasticsearch.org/elasticsearch/1.3/debian stable main
    

    Run apt-get update and the repository is ready for use. You can install it with :

    apt-get install elasticsearch
    

    For RHEL/CentOS Users: Download and install the Public Signing Key

    rpm --import http://packages.elasticsearch.org/GPG-KEY-elasticsearch
    

    Add the following in your /etc/yum.repos.d/ directory in a file named (for example) elasticsearch.repo

    [elasticsearch-1.3]
    name=Elasticsearch repository for 1.3.x packages
    baseurl=http://packages.elasticsearch.org/elasticsearch/1.3/centos
    gpgcheck=1
    gpgkey=http://packages.elasticsearch.org/GPG-KEY-elasticsearch
    enabled=1
    

    And your repository is ready for use. You can install it with :

    yum install elasticsearch
    

    Install Elasticsearch bind for python:

    pip install elasticsearch
    

Start Server

  1. If you want to use this application on a production site, use Apache with mod_wsgi.

    Tip: Get more information at https://docs.djangoproject.com/en/1.6/howto/deployment/wsgi/modwsgi/

  2. If you just want to experiment with this application, just use following command:

    python manage.py runserver
    

    If you will get following output,

    May 14, 2014 - 04:50:57
    Django version 1.6.4, using settings 'BioDesigner.settings'
    Starting development server at http://127.0.0.1:8000/
    Quit the server with CONTROL-C.
    

    The application is deployed successfully. And you can use the application by visit http://127.0.0.1:8000 in web browser.

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