tlb 12/25/97; changed parallel installation procedure
tlb 8/2/96; added MAST
tlb 3/1/96; created

==================================
SUPPORTING THE MEME SYSTEM WEBSITE
==================================

This document describes how to support a MEME SYSTEM WEBSITE.

=============
PREREQUISITES
=============
1. LAM-MPI  available at http://www.lam-mpi.org
    or
   MPICH available at http://www-unix.mcs.anl.gov/mpi/mpich
2. CGI.PM available at http://www.cpan.org or using "perl -MCPAN -e 'shell' "

=======================
THE MEME SYSTEM WEBSITE
=======================

The WEBSITE consists of a 
	1) HOMEPAGE, 
	2) MEME CLIENT, 
	3) MEME SERVER, 
	4) MEME,
	5) MAST CLIENT,
	6) MAST SERVER and
	7) MAST.

Note:  In what follows, the following names are used and the ACTUAL NAMES 
should be SUBSTITUTED when the installation is done:

MEME.X.Y        - current version of MEME, ie, "meme.2.2"
WEB_ADDRESS     - web address of MEME homepage
WEB_DIR         - directory where homepage lives
MEME_CPU        - name of CPU where MEME and the MEME server run
MEME_DIR	- name of directory where MEME and the MEME server are installed
MAST_CPU        - name of CPU where MAST and the MAST server run
MAST_DIR	- name of directory where MAST and the MAST server are installed

=========================
INSTALLING A NEW HOMEPAGE
=========================

The HOMEPAGE and MEME and MAST CLIENTS are installed in directory
	WEB_DIR/meme 		#in RH-Linux, it is typically /var/www/html/meme
by the following procedure:

	$ cd WEB_DIR/meme
	$ tar xvf MEME.X.Y.tar	
	$ cd MEME.X.Y
	$ bin/install homepage	# prompts for MEME and MAST <socket #> and 
				# <host name>
	> <socket #>		# MEME socket number; check file
				# /etc/services to make sure
				# socket number is not already used
	> <meme_host> 		# name of the cpu where MEME will run
	> <socket #>		# MAST socket number; check file
				# /etc/services to make sure
				# socket number is not already used
	> <mast_host>		# name(s) of the cpu(s) where MAST will run


============================
INSTALLING A NEW MEME SERVER
============================

The MEME SERVER and MEME are installed on a the MEME_CPU as follows.

1) Install:
	$ cd MEME_DIR
	$ tar xvf MEME.X.Y.tar
	$ cd MEME.X.Y

   You will be asked for socket numbers and host names by the next command.  
   Enter the same ones as you specified when you installed the homepage.
   Specify "parallel" and "-p" below only if you are installing on a
   parallel platform that has MPI installed.

	$ bin/install server		# creates the MEME and MAST servers
	$ bin/install client		# do only if meme server is on a
					# different cpu than web server
	$ bin/install meme [parallel]	# creates MEME and MAST
	$ bin/runtests [-p <n>]		# tests MEME and MAST

        bin/runtests [-p <n>]

   Specify "parallel" and "-p <n>" above only if you are installing on a 
   parallel platform that has MPI installed.  <n> is the number of processes
   you want the parallel version to use.

   CAUTION: Edit the bin/meme.init.start file following the instructions given in it.

   Now start the meme server running--
        $ bin/meme.init.start

   Insure that the server gets restarted if the system crashes by
   using crontab -e to add the following line to the crontab:

	0,10,20,30,40,50 * * * * MEME_DIR/bin/meme.init.start > /dev/null 2>&1


============================
INSTALLING A NEW MAST SERVER
============================

The MAST SERVER and MAST are installed on the MAST_CPU as follows.

1) Install: 
	$ cd MAST_DIR
	$ tar xvf MEME.X.Y.tar
	$ cd MEME.X.Y

   You will be asked for socket numbers and host names by the next command.  
   Enter the same ones as you specified when you installed the homepage.
	$ bin/install server		# creates the MEME and MAST servers
	$ bin/install client		# do only if mast server is on a
					# different cpu than web server
	$ bin/install meme 		# creates serial MEME and MAST
	$ bin/runtests [-p]		# tests MEME and MAST

   Edit the bin/mast.init.start following the instructions given in it.

   Now start the mast server running--
        $ bin/mast.init.start

   Insure that the server gets restarted if the system crashes by
   using crontab -e to add the following line to the crontab:

	0,10,20,30,40,50 * * * * MAST_DIR/bin/mast.init.start > /dev/null 2>&1

2) Set up the link to the MAST databases:
	$ cd MAST_DIR
	$ ln -s <mast-databases-directory> mast_databases

3) Download the MAST databases.  You should make a cron job do this on a regular basis:
	$ cd mast_databases
	$ bin/update_mast_databases <your email address> . < bin/mast_db.list
   You will receive mail when the download is complete.



======================
TESTING A NEW HOMEPAGE
======================

Check that the homepage, clients, servers, MEME and MAST are working as follows.
In your browser (ie, netscape), access:

	http://WEB_ADDRESS/MEME.X.Y

	1) Check that all of the links work.
	2) Submit sequences to MEME and check that the results are
	   correct (MEME didn't bomb) and are emailed back to you.
	3) Submit a MEME file to MAST and check that the results mailed
	   back to you are correct.


=========================
ACTIVATING A NEW HOMEPAGE
=========================

Make the new homepage the one seen by the world as follows:

1) Create a new index for the main website directory:
        $ cd WEB_DIR
        $ MEME.X.Y/bin/mkindex -d MEME.X.Y