Environment Construction Tutorial

• Credit to Jiawei Li

To run GSV and mGSV, you need to install PHP5.3.20 or higher but no more than PHP5.50 + Apache or Nginx + MySQL and make sure that PHP has the MySQL extension and GD extension enabled. Because mGSV needs to use MySQL extensions to operate on MySQL, store collinear data and use the GD library to draw the picture.

If your existing php version is php7 or is not installed PHP, you should build an environment that can use PHP5 because PHP5 and PHP7 have big differences, PHP7 has abandoned some extension libraries. For example, the mysql extension in PHP5 has been deprecated in PHP7 and replaced with the mysqli extension. This will causes a series of mysql extension functions in the GSV and mGSV script code to be unavailable, causing an error.

The following is a tutorial on configuring the environment required to run the GSV and mGSV in CentOS.

• Note: Requires root privileges

Section I: Install Nginx

• Install gcc and g++

yum -y install gcc automake autoconf libtool make
yum install gcc gcc-c++

• Install PCRE

cd /usr/local/src
wget ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-8.39.tar.gz
tar -xzvf pcre-8.39.tar.gz
cd pcre-8.39
./configure
make
make install

• Install zlib

cd /usr/local/src
wget http://zlib.net/zlib-1.2.11.tar.gz
tar -xzvf zlib-1.2.11.tar.gz
cd zlib-1.2.11
./configure
make
make install

• Install Nginx

cd /usr/local/src
wget http://nginx.org/download/nginx-1.1.10.tar.gz
tar -zxvf nginx-1.1.10.tar.gz
cd nginx-1.1.10
./configure
make
make install

• Configure Nginx
• Because I installed Apache before and Apache uses port 80. So I configured Nginx to use port 8089.

vim /usr/local/nginx/conf/nginx.conf

• Running Nginx

/usr/local/nginx/sbin/nginx -c /usr/local/nginx/conf/nginx.conf

• Put the web file in /usr/local/nginx/html/ . You can now successfully access the web page in the browser. (i.e., http://YOUR_IP:8089/)
• You will see the following:

Section II: Install PHP

• Install ibpng and freetype

conda install -c conda-forge libpng
conda install -c conda-forge freetype

• Install GD library

wget https://github.com/libgd/libgd/releases/download/gd-2.2.4/libgd-2.2.4.tar.gz

tar -xzvf libgd-2.2.4.tar.gz
cd libgd-2.2.4
./configure --prefix=/usr/local/gd2 --with-png --with-freetype
make
make install

• Download the required PHP version

wget http://museum.php.net/php5/php-5.3.20.tar.gz

• Compile PHP

tar -xzvf php-5.3.20.tar.gz
cd php-5.3.20
./configure --enable-fpm --enable-mysqlnd --with-mysql=/opt/lampp/ --without-sqlite --without-pdo-sqlite --with-gd --with-freetype-dir=/usr/include/freetype2/freetype/
make
make install

• Obtain and move configuration files to their correct locations

cp php.ini-development /usr/local/php-5.3.20/php.ini

• Load up php.ini

vim php.ini

• Open the mysql and gd extensions. Find and modify the following:

• Locate cgi.fix_pathinfo= and modify it as follows:

Section III: Configure Nginx and php-fpm so that web pages can use php5 that you just installed

• Obtain and move php-fpm.conf to their correct locations

cp /usr/local/etc/php-fpm.conf.default /usr/local/sbin/php-fpm.conf

• Enter /usr/local/sbin and you should see php-fpm and php-fpm.conf

cd /usr/local/sbin

• Modify the php-fpm.conf file

• Running php-fpm

/usr/local/sbin/php-fpm

• Modify the nginx.conf file

cd /usr/local/nginx/conf
vim nginx.conf

• Restart the Nginx

/usr/local/nginx/sbin/nginx -s reload

• Write a PHP script to test if the configuration is successful

cd /usr/local/nginx/html/
vim phptest.php

input:

<?php
phpinfo();
?>

• Access phptest.php scripts through your browser (i.e., http://YOUR_IP:8089/phptest.php)
• Displays this content indicating that the configuration was successful.

mGSV Installation Guide

System Requirements

The current version of Genome Synteny Viewer was only tested on Ubuntu 10.04 OS. The minimum requirements include:

• Apache 1.3 or higher (http://www.apache.org)
• PHP 5.3.20 but no more than PHP5.50 (http://www.php.net/)
• MySQL 5.0 or higher (http://dev.mysql.com/)
• GD library. (http://php.net/manual/en/book.image.php)

NOTE：PHP must have the MySQL extension and GD extension enabled

If you successfully completed the above Environment Construction Tutorial, you have everything installed.

MySQL Database Setup

• Log into MySQL, replace with your root password

mysql -u root -p <password>

• Create 'mgsv' database

CREATE DATABASE mgsv;

• Create a user 'mgsv'

CREATE USER 'mgsv'@'localhost' IDENTIFIED BY 'mgsvpass';

• Set privileges to 'mgsv' to use database

GRANT SELECT, INSERT, CREATE, DROP ON mgsv.* TO 'mgsv'@'localhost';

• Create table "userinfo" in 'mgsv' database by executing the following MySQL command

use mgsv;

CREATE TABLE IF NOT EXISTS `userinfo` (
	`id` int(10) NOT NULL AUTO_INCREMENT,
	`email` text NOT NULL,
	`hash` text NOT NULL,
	`synfilename` text NOT NULL,
	`annfilename` text NOT NULL,
	`url` text NOT NULL,
	`session_id` text NOT NULL,
	`annImage`   int(5) NOT NULL,
	`create_on` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,
	PRIMARY KEY (`id`)
) ENGINE=MyISAM  DEFAULT CHARSET=latin1 AUTO_INCREMENT=3 ;

Set up mGSV

• Download the source code

git clone https://github.com/qunfengdong/mGSV.git

• Create a folder named mgsv in the DocumentRoot of Nginx web server. By default, the DocumentRoot of Nginx is /usr/local/nginx/html/

cd /usr/local/nginx/html
mkdir mgsv
chmod 777 mgsv

• Enter 'mgsv' directory and create a folder named tmp. Execute a Linux command to change permission for 'tmp' folder. It has to be world accessible to store the uploaded files.

cd mgsv
mkdir tmp
chmod -R 777 tmp

• Move all files under the downloaded mGSV folder to the mgsv folder
• Under 'mgsv' folder you should see a file called 'Arial.ttf', Copy it to /usr/share/fonts/truetype/, you may need the sudo privilege, talk to your system administrator if necessary.

cp Arial.ttf /usr/share/fonts/truetype/

• Modify the setting.php file. File path is /usr/local/nginx/html/mgsv/lib/

cd /usr/local/nginx/html/mgsv/lib/
vim setting.php

Add the following information:

$database_name = 'mgsv';
$database_user = 'mgsv';
$database_pass = 'mgsvpass';
$database_host = 'localhost';

• This completes installation, you can now open mgsv/index.php (i.e., http://<YOUR_SERVER_DOMAIN_NAME>/mgsv/index.php)