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(01-A) Please read before installing - Architecture
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(01-B) Please read before installing - Tested OS
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(02-A) External Dependencies - ConfBuster
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(02-B) External Dependencies - Python
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(02-C) External Dependencies - Apache
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(02-D) External Dependencies - PHP
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(02-E) External Dependencies - MySQL MariaDB
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(03-A) Web Server - Installation
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(03-B) Web Server - Deployment
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(03-C) Web Server - Configuration
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(04-A) Job Preparation Server - Installation
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(04-B) Job Preparation Server - Deployment
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(04-C) Job Preparation Server - Configuration
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(05-A) Compute Server - Installation
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(05-B) Compute Server - Deployment
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(05-C) Compute Server - Configuration
(01-A) Please read before installing - System Architecture
The ConfBuster Web Server system was made to be
installed on two different physical computers :
Computer 1 : * WebServer
Computer 2 : * JobPreparation Server
* Compute Server
However, it is possible to install the three software
servers on the same computer.
Please refer to the UML Architecture Diagram located in the
ConfBuster Web Server distribution for additional details.
(01-B) Please read before installing - Tested OS
The installation/deployment/configuration instructions were
tested on the following operating system :
Linux Mint 18.3 Cinnamon 3.6.7 64-bits
(02-A) External Dependencies - ConfBuster
* Install ConfBuster
- The lastest version
https://github.com/patricklague/ConfBuster
At the end of the installation, ConfBuster should be in
the system $PATH (eg. /usr/bin) with all its dependencies
installed.
(02-B) External Dependencies - Python
* Install Python 2
- Version >= 2.7.12
sudo apt install python
* Install Python 2 MySQL Module
- Version >= 1.3.7
sudo apt install python-mysqldb
(02-C) External Dependencies - Apache
* Install the Apache HTTP Server
- Version >= 2.4.18
sudo apt install apache2
* Install the Apache PHP Module
sudo apt install libapache2-mod-php7.0
(02-D) External Dependencies - PHP
* Install PHP-5
- Version (PHP-5) >= 5.4.45
sudo apt install php7.0
* Install PHP MySQL Module
sudo apt install php7.0-mysql
(02-E) External Dependencies - MySQL MariaDB
* Install MySQL MariaDB Database Server
- MySQL Version >= 15.1
- MariaDB Version >= 10.0.33
sudo apt install mariadb-server-10.0
(03-A) Web Server - Installation
..i) Create a folder named "ConfBuster" into the "/var/www" directory.
sudo mkdir /var/www/ConfBuster
.ii) Move the "WebServer" folder of the GitHub Distribution into the directory "/var/www/ConfBuster".
sudo mv WebServer /var/www/ConfBuster/
(03-B) Web Server - Deployment
...i) Open the Apache configuration file.
sudo nano /etc/apache2/apache2.conf
..ii) Configure the home page of the web site by adding the following lines at the end of the file:
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Directory Index
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# List of all possible file name that can be
# used as a home page.
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<IfModule dir_module>
DirectoryIndex index.html index.php \
Home.html home.html home.php
</IfModule>
.iii) Open the Apache port configuration file.
sudo nano /etc/apache2/ports.conf
..iv) Configure the port if needed (default 80).
Listen 80
...v) Open the Apache Virtual Server configuration file.
sudo nano /etc/apache2/sites-available/000-default.conf
..vi) Configure the port used by the Virtual server match the one configured in step iv) by making sure the "VirtualHost" start tag as the following syntax:
<VirtualHost *:80>
.vii) Configure the folder path of the web site by changing the "DocumentRoot" statement by this one :
DocumentRoot /var/www/ConfBuster/WebServer
viii) Reboot the Apache server
sudo /etc/init.d/apache2 restart
(03-C) Web Server - Configuration
.i) Open the script used for redirecting the user's data to the Job Preparation Server :
sudo nano /var/www/ConfBuster/WebServer/DataReception.php
ii) Edit the URL corresponding to the location of the "ComputeJobPreparation.php" file in the JobPreparationServer.
If the JobPreparationServer is on another computer :
http://***.***.***.***:8080/BusinessLayer/ComputeJobPreparation.php
If the JobPreparationServer is on the same computer :
http://127.0.0.1:8080/BusinessLayer/ComputeJobPreparation.php
(04-A) Job Preparation Server - Installation
.i) Create a folder named "ConfBuster" into the "/var/www" directory.
sudo mkdir /var/www/ConfBuster
ii) Move the "JobPreparationServer" folder of the GitHub Distribution into the directory "/var/www/ConfBuster"
sudo mv JobPreparationServer /var/www/ConfBuster/
(04-B) Job Preparation Server - Deployment
..i) Open the Apache port configuration file
sudo nano /etc/apache2/ports.conf
.ii) Add the following line at the end of the file
Listen 8080
iii) Open the Apache Virtual Server configuration file
sudo nano /etc/apache2/sites-available/000-default.conf
.iv) Configure the port used by the Virtual server by making sure the "VirtualHost" start tag as the following syntax :
<VirtualHost *:8080>
..v) Configure the folder path of the web site by changing the "DocumentRoot" statement by this one :
DocumentRoot /var/www/ConfBuster/JobPreparationServer
.vi) Reboot the Apache server.
sudo /etc/init.d/apache2 restart
(04-C) Job Preparation Server - Configuration
..i) Open the file script used for sending email :
sudo nano /var/www/ConfBuster/JobPreparationServer/BusinessLayer/Mail/MailManager.py
.ii) Edit the Mailling information located in the private attributes of the MailManager class.
iii) Open the database manager :
nano /var/www/ConfBuster/JobPreparationServer/DatabaseLayer/DatabaseManager.php
.iv) Edit the database connection credentials located in the private attributes of the DatabaseManager class.
(05-A) Compute Server - Installation
Since the server has to be started manually, it does not
matter where the folder is located. For convenience purpose,
it is recommended to follow this optional step :
i) Move the "ComputeServer" folder of the GitHub Distribution into the directory "/var/www/ConfBuster"
sudo mv ComputeServer /var/www/ConfBuster/
(05-B) Compute Server - Deployment
..i) Open the database installation script :
nano /var/www/ConfBuster/ComputeServer/DatabaseLayer/Database_DDL_DML_DCL_Script.sql
.ii) Configure the credential of the user at the end of the file.
iii) Install the database with the following command :
sudo mysql -u root -p < /var/www/ConfBuster/ComputeServer/DatabaseLayer/Database_DDL_DML_DCL_Script.sql
Input upon password prompt :
root
.iv) Reboot the Database server.
sudo /etc/init.d/mysql restart
..v) Configure the Queue and the Compute Server by editing the corresponding parameters located in the following file :
sudo nano /var/www/ConfBuster/ComputeServer/BusinessLayer/QueueManager.py
.vi) Start the Compute Server.
sudo python /var/www/ConfBuster/ComputeServer/BusinessLayer/QueueManager.py
(05-C) Compute Server - Configuration
..i) Open the file used for sending email :
sudo nano /var/www/ConfBuster/ComputeServer/BusinessLayer/ManagerClasses/MailManager.py
.ii) Edit the Address of the Mail SMTP Server located in the private attributes of the MailManager class.
iii) Open the database manager :
nano /var/www/ConfBuster/ComputeServer/DatabaseLayer/DatabaseManager.py
.iv) Edit the database connection credentials located in the private attributes of the DatabaseManager class.
ConfBuster Web Server Copyright (C) 2018 Gabriel Bégin, Xavier Barbeau, Antony T. Vincent and Patrick Lagüe
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
Bégin, G., Barbeau, X., Vincent, A.T. & Lagüe, P.
ConfBuster Web Server: a free web application for macrocycle
conformational search and analysis (in preparation).
Barbeau, X., Vincent, A.T. & Lagüe, P., (2018).
ConfBuster: Open-Source Tools for Macrocycle Conformational
Search and Analysis.
Journal of Open Research Software. 6(1),p.1.
DOI: http://doi.org/10.5334/jors.189