Instructions to run

Client Dependencies

install virtualbox 4.3

wget http://download.virtualbox.org/virtualbox/4.3.16/virtualbox-4.3_4.3.16-95972~Ubuntu~lucid_amd64.deb
sudo dpkg -i virtualbox-4.3_4.3.16-95972~Ubuntu~lucid_amd64.deb

manually install ubuntu virtual machine ( ubuntu-14.04.1-desktop-amd64.iso ) install vim and do some necessary configuration steps

Server Dependencies

install a few of dependencies

install gcc

sudo apt-get install build-essential

install make

sudo apt-get install make

install Apache Tomcat 7 on ubuntu 14.04

sudo apt-get update

sudo apt-get install tomcat7

Apache Tomcat Tools - optional

sudo apt-get install tomcat7-docs tomcat7-admin tomcat7-examples

Install Java Development Kit (Optional)

sudo apt-get install default-jdk

install ant and git

In addition to JDK, the Tomcat documentation suggests also installing Apache Ant, which is used to build Java applications, and a source control system, such as git. Let's install both of those with the following command

sudo apt-get install ant git

install mysql server 5.6

Note: set your root pass for mysql

sudo apt-get install mysql-server-5.6

download mysql-connector-java-5.1.32.tar.gz for mysql connector http://dev.mysql.com/downloads/connector/j/5.1.html

Setup portal & database

Note: currently jsmol fils have been integrated into hotspot3d_port repo

install maven for package

sudo apt-get install maven2

clone hotspot3d_portal

git clone https://github.com/ding-lab/hotspot3d_portal.git
cd hotspot3d_portal
mvn package
cp -r target/HotSpot3D /var/lib/tomcat7/webapps

mysql database import using 3d_proximity databse identified by 'YouChoose'

mysql -u root -p
mysql> create database 3d_proximity;
mysql> CREATE USER '3d_proximity'@'localhost' IDENTIFIED BY 'YouChoose';
mysql> GRANT ALL PRIVILEGES ON 3d_proximity . * TO '3d_proximity'@'localhost';

import 3d_proximity data into database

mysql -u root -p < src/main/config/mysql/3d_proximity.sql 

Note: you can update the latest mysql data using mysqldump