BIOLAD-DB INSTALLATION INSTRUCTIONS
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The files and programs (the schema and starter data, DEB, FRED, and the genotype
loader) included in the BiolAD_DB system are freely available for academic
and nonprofit use only.  A license is required for the commercial download 
and/or installation of the copyrighted programs.  Licensing inquires should 
be directed to The Rockefeller University Office of Technology Transfer
(212-327-8266) 1230 York Avenue, New York, New York 10021.  Copyright ©2006
is held by The Rockefeller University.  Any publications resulting from the use
of these programs or modifications of these programs should cite the article: 
Nielsen, D.A., Leidner, M., Haynes, C., Krauthammer, M., and Kreek, M.J. (2006) 
The BiolAD-DB System – An Informatics System for Clinical and Genetic Data. 
In preparation.  Questions about the code should be addressed to 
David A. Nielsen, Ph.D. at nielsen@rockefeller.edu.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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For more information visit the BiolAD-DB website at http://www.rockefeller.edu/biolad-db/
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These are the steps required to install and setup the BiolAD-DB system.  


1) MySQL installation:
	If you already have MySQL installed, please skip this step.
	Download and install the MySQL database sever and standard clients from:
		http://www.mysql.com
	Please take note of the MySQL version you are choosing or already have 
	   running as this may be needed later on.
	If you are compiling MySQL yourself please note, we make use of the InnoDB
	   functionality so make sure it is available.

2) Copy the schema and starter data:
	Download the schema and starter data from http://www.rockefeller.edu/biolad-db/

3) Start Database service:
	Start and log into MySQL by opening the MySQL Command Line Client.

4) Create a new database:
	>> create database <database name>;

5) Load the schema into the database:
	>> use <database name>;
	>> \. <path to schema file>
		The above statment creates the database schema needed for 
		   the project.
		Please ignore the warnings regarding the syntax or change
		   all occurrances of 'TYPE=InnoDB' to 'ENGINE=InnoDB'

6) Load the initial database data:
	>> \. <path to starter data>

7) Create a new MySQL user named 'debuser'
	>> GRANT SELECT,UPDATE,INSERT,DELETE ON <database name>.* TO 'debuser'@'localhost%' IDENTIFIED BY '<insert password here>';
please note: If you are not running your Mysql database locally, then you need to modify this command to point to the host of your database.

8) Python installation:
	DEB requires the Python Interpreter.

	The following Python components are required: 
	a) Python v2.3 or higher:
		Download and install from http://www.python.org. 
		Please note the version you install as some sub-components are
		   version coordinated.
	b) MySQL for Python:
		(http://sourceforge.net/projects/mysql-python)
		The windows version for Python v2.4 is called 
		   -> MySQL-python.exe-1.2.0.win32-py2.4.zip
		Note: There are more recent versions available but they do not include a windows installer.
	c) wxPython: A set of Python extension modules that wrap the cross-platform GUI 
	      classes from wxWindows (wxPython v2.5.2.* or v2.5.3.*)
		Do NOT use anything above v2.5.3.  It has not been tested and most likely will not work
		Older versions can be downloaded from 
		   http://sourceforge.net/projects/wxpython/
		Choose the link to Download wxPython2.5-win32-ansi-2.5.%.%-py2%.exe
		   where the py2% matches your python version (py24 for python 2.4).
		Run the executable to install.
	d) py2exe v0.5 or higher:
		Optional.
		Note: py2exe is only required if you wish to generate executables
		(http://py2exe.sourceforge.net/).
	e) Python Extensions for Windows:
		(http://sourceforge.net/projects/pywin32/)

9) DEB installation:
	a) Unpack the DEB distribution .zip file to a directory of your choice.
	b) Modify the deb.ini file:
		Change 'db' to equal the database name previously created.
		Change hosts to equal a comma separated list of possible MySQL 
		   hosts.
			Note: if you are running a local MySQL server, the host
			   name is localhost or 127.0.0.1
		Optional:  Set the host default database to be the name of the
		   default host.
		Add any ethnicities you plan to use.

10) Run the DEB program:
 	a)  The program may be started from a command prompt by 
		changing to the DEB install directory and typing the command:
			python interface.py
		Note: If the python executable is not in your system path you will need
		to give the full path to the file:
			C:\Python24\python interface.py
	
	Or

	b) Optional: If you want to create an executable file run the setup.py
		script as follows (downloaded in step 8.d):
			From a command prompt change to the DEB install 
			   directory and type command 'python setup.py py2exe'.
		This will create a dist directory containing the executable 'deb.exe' and all
		other necessary files.

	c) Use the user 'debuser' and the password you supplied in step 7 to log in