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This file is a preliminary Readme for the Alcohol Research Integrator Analysis Suite

Last updated: 6/29/2009

Files included in this package:
-------------------------------
-README - This file
-genedb.pl - The Alcohol Research Integrator, the web based interactive database system
-normalize.pl - A batch non-linear normalization program for cDNA based arrays
-standardize.pl - Standardizes multiple arrays based on a common reference
-annotatate.pl - breaks a single annotation field into many annotation columns
-filter.pl - Filters out genes with sufficiently sparse data
-stats.pl - Performs t-test, f-test, FDR, and PLS analyses on standardized microarray data
-loaddb.pl - loads a completely analyzed dataset into an already set up MySQL database for browsing by genedb.pl
-images - images directory for the web-based programs
-perllib - a directory of perl modules written for the aridb suite
-pls - an R pls package written by Mike Denham
-md5crypt - generates an MD5 hash from a password that can be used to set up
	    the web-based genedb.pl system.
-style.css - the style definitions for the web-based system

Although the source code doesn't have it there yet, all code in this package 
is protected under the Gnu Public License. Any changes made to the source
code should be made available to the original author via the SourceForge website:

http://sourceforge.net/projects/aridb

Installation
------------

Currently, installation of the ARIDB system is complex and difficult and many 
steps will require the expertice of a seasoned system administrator to complete
This is a brief overview of the process. A more detailed installation instruction
set, as well as a first-run section of the genedb.pl program, will come later.

1) Make sure that perl 5.8 and above is installed on the system
2) Make sure that Apache 2.0 and above is installed on the system
3) Make sure that MySQL 4.0 and above is installed on the system
4) Make sure that gnuplot 4.0 and above is installed on the system
5) Enable mod_ssl and create a 128-bit SSL certificate using openssl
6) Move normalize.pl, standardize.pl, annotate.pl, stats.pl, and loaddb.pl to 
   /usr/local/bin, but remove the .pl from the end. This puts them in the systems
   default path.
7) Move genedb.pl to the base cgi-bin directory for the secure apache server.
8) Alter the variables in the first section of the genedb.pl source code from lines 6 - 52.
9) Create the following directories under the directory specified under the $TMPHDIR variable:
	-plsimg
	-tmp
	-genedbimg
10) Move the images directory to this same location
11) Move the style.css file to this same location
12) In MySQL, do the following:
	-create the usernames and passwords that you entered into the config section 
	 of genedb.pl (hint: use grant)
	-Enter the following commands:

create database genedbs;
use genedbs;
create table admin (user text, dbs text, perm enum('admin','user','guest');
create table dblist (db text, descr text, access enum('open','password','restricted');
create table passwd (user text, password blob, valid blob);
quit

13) Execute the program md5crypt.pl in this directory and enter a password for yourself.
14) Using the encrypted password that was just created, go back to MySQL and enter the
following commands:

use genedbs;
insert into passwd (user,password) values ("yourusername","encryptedpassword");
insert into admin (user,perm) values ("yourusername","admin");
quit

15) Make sure that the following Perl modules are installed on the system:
	-Bundle::MySQL
	-CGI::Lite
	-Term::ANSIColor
	-Term::ReadKey
	-Text::Wrap
	-Statistics::Distributions
	-Math::Complex
	
	These packages can be installed by executing the command:

	perl -MCPAN -e shell

	as root. Follow the setup instructions, then type:

	install packagename

	where packagename is the perl module from above.

16) Copy the perllib directory to /usr/local/bin
17) Make sure that R is installed on the system (http://www.r-project.org/)
18) Make sure that the entire BioConductor distribution is installed into R (http://www.bioconductor.org/)
19) Install the pls R module from the pls directory in this directory
20) Try to manually run all of the software packages and see if you get errors. If you
    do, correct them as necessary
21) Log into the aridb with your new username and password under the *Admin section to make
    sure that you have proper access

DISCLAIMER:
-----------

This installation process is untested, is totally from memory, and probably won't work the first time!
If you encounter a part of the installation that isn't working, please send me email and I'll try
to help you iron out the problems. Perhaps one day, I'll create an installer, but for now, I
have to trust that you know enough about how to administer a Linux system to accomplish this
on your own, or that you have a sysadmin capable of helping you.

Good luck!

--Ari
Source: README, updated 2010-02-02