INSTALL.txt

Installation on a CentOS Linux Distro.

	MYSQL server:
		- install mysql server with yum or direct rpm source. Import the database from a dump
		mysql BEAST_dev < beast_dump.sql


	Install Apache:
		- check httpd running.
		- Add Listen beast.soe.ucsc.edu:80 to /etc/httpd/conf/httpd.conf

	Open Firewall to allow connections for port 80:
		- append rule: 
			-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 80 -j ACCEPT
		to /etc/sysconfig/iptables
		and then /etc/init.d/iptables restart

	Troubleshooting: 
		- try telneting through port 80 from another machine. If it's blocked, or if you 
		get a 'no route to host' error, the firewall (iptables is probably misconfigured)
	


	Installing GIT:	
	

		- Generate a ssh public key using ssh-keygen on the machine, then copy and paste the
		.pub file to github (import ssh keys).

	PERL Packages:

		- requires 5.8.x or later and DBI/DBD and SQL packages, along
		  with JSON.pm

	Install BEAST:
	
		- create sysbio user and allow it to modify /var/www/html and
		  /var/www/cgi-bin.
		- create /projects/sysbio/beast
			/projects/sysbio/beast/perllib
		run 'make soe' to install from the git repository

	SQL Config: 
		- mysql --user=root mysql
		- add a new read-only beast user, set the passwd, : CREATE
		  USER 'beast_user'@'localhost' IDENTIFIED BY 'passwd';
		- GRANT SELECT ON *.* TO 'beast_user'@'localhost'

	Java Compatability:

		- Install ant, javac and java	


	SOE Libs:

		install cluster-eisen, sets_overlap.pl and the perl/lib
		directory from sysbio

	DB Indexing:

		- re index

	LINUX Caveats:

		- By default, SeLinux does not allow httpd to make connections
		to the network - even to localhost. You need to run the
		following command as root to fix this:
		 $ setsebool -P httpd_can_network_connect=1

		Otherwise you'll get a 'permission denied' error when you
		try to connect from httpd, which can drive you crazy trying to
		debug, as it has nothing to do with the code itself!