Installation of the web application for handling results and exchanging other data (e.g. help files, software packages)
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The application has been tested both on linux (CentOS 6.4) and windows (Windows7). A basic knowledge of doing installations on at least one of the operating systems is assumed.

The webpage for results and management requires a set of software which is available for free. The application was tested with the specified versions but newer versions may also work.

- Apache-httpd-Webserver 2.2 can be downloaded from http://httpd.apache.org/. Please follow the installation instructions available from there.

- PHP 5.3 is available from http://php.net/downloads.php (newer versions should also work). Please follow the installation instructions available from there.

- MySQL 5.5 and MySQL-Workbench 5.2  (if not already done during intallation of the PhenotypingSchemeComposer web application) can be downloaded from http://dev.mysql.com/downloads/. Please follow the installation instructions available from there. MySQL-Workbench is not absolutely necessary but makes all administration tasks much easier. You should create one database user which will be used for making the connection from the website to the database. This user should be allowed to insert, select, update and delete database entries but nothing more.
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Setting up the database.
- Create a database 'phenotyper'.
- Load the dump file phenotyper_database.sql to the MySQL instance.

Setting up the web application.
- Copy the html - directory to the htdocs directory of your Apache-httpd installation and customize the httpd.conf file.
- Customize configurations:
	+ in html/database/app/config/database.php:
		# modify the default settings to reflect your database configuration: login, password, database name
		# make directory html/database/app/tmp and all below writable to apache user and group
	+ File upload configuration:
		# html/database/app/config/bootstrap.php
			* FileUpload.uploadDir is the path on your webserver. In its current configuration, this would be app/webroot/files/
			* FileUpload.viewDir is the relative URL to retrieve the files. This would be http://localhost/files/
	+ in html/database/app/config/core.php
		# there is a default hash key which has been used to create the data for the default user you will find in the dumped database:
	################################################################################
		/**
			* A random string used in security hashing methods.
		*/
			Configure::write('Security.salt', 'j584934jmtu034ß0msd08496mdfög');
	#################################################################################
	
		Using this key, you get the following password (the hashed text) for the default user:

			Clear text: glueck
			Key: j584934jmtu034ß0msd08496mdfög
			Hashed text: 5f6fd3b27872e2e1e76603ec872d0d5ee3f1b6a0
	
		# to generate the initial user entries with a new hash key please use HashGenerator.jar
		
		java -jar HashGenerator.jar <clear text sring> <has key> [<optional output file>]
		
		These user entries have not to be inserted in the people table using a database management system (can be the mysql command line version or MySQL Workbench). As soon as the web application has been set up all new users can be created using the web application.