File	Date	Author	Commit
cgi-bin	2009-08-21	Nils Homer	[c5b58f] Adding in complimentary program: BFAST server.
config	2009-08-21	Nils Homer	[c5b58f] Adding in complimentary program: BFAST server.
html	2009-08-21	Nils Homer	[c5b58f] Adding in complimentary program: BFAST server.
AUTHORS	2009-08-21	Nils Homer	[c5b58f] Adding in complimentary program: BFAST server.
COPYING	2009-08-21	Nils Homer	[c5b58f] Adding in complimentary program: BFAST server.
ChangeLog	2009-08-21	Nils Homer	[5fda24] Adding compatibility with BFAST >= 0.5.5
INSTALL	2009-09-26	Nils Homer	[ee5192] Updating BFAST SERVER to be compatible with BFA...
LICENSE	2009-08-21	Nils Homer	[c5b58f] Adding in complimentary program: BFAST server.
Makefile.am	2009-10-06	Nils Homer	[ce674b] Redoign the updates to make bfast-server compat...
NEWS	2009-08-21	Nils Homer	[c5b58f] Adding in complimentary program: BFAST server.
README	2009-10-06	Nils Homer	[3751f2] Adding space declaration in the input file for ...
autogen.sh	2009-08-21	Nils Homer	[c5b58f] Adding in complimentary program: BFAST server.
bfast_client.c	2009-09-26	Nils Homer	[ee5192] Updating BFAST SERVER to be compatible with BFA...
bfast_client.h	2009-08-21	Nils Homer	[c5b58f] Adding in complimentary program: BFAST server.
bfast_data.c	2010-02-10	Nils Homer	[2095db] Merge branch 'master' of ssh://bfast.git.source...
bfast_data.h	2009-09-26	Nils Homer	[ee5192] Updating BFAST SERVER to be compatible with BFA...
bfast_netlib.c	2009-09-26	Nils Homer	[ee5192] Updating BFAST SERVER to be compatible with BFA...
bfast_netlib.h	2009-09-26	Nils Homer	[ee5192] Updating BFAST SERVER to be compatible with BFA...
bfast_server.c	2009-09-26	Nils Homer	[ee5192] Updating BFAST SERVER to be compatible with BFA...
bfast_server.h	2009-08-21	Nils Homer	[c5b58f] Adding in complimentary program: BFAST server.
configure.ac	2009-10-06	Nils Homer	[ce674b] Redoign the updates to make bfast-server compat...

Read Me

Welcome to bfast server.

bfast server is copyrighted software. Please see the file LICENSE for details.

For installation directions, please see:
INSTALL

== QUICK START GUIDE ==

This guide is meant to describe some of the ambiguous arguments to the 
BFAST server.  The intention is to replace this with a full manual. Please
send suggestions to nhomer@cs.ucla.edu.

The user must give the list of references and indexes to the BFAST Server.
Each line of the reference genome list or the index list must include at 
least two space/tab seperated items:
	1. path and filename to the reference genome (.brg) and index (.bif).
	2. the id to use (typically the name of the genome described).
For the reference genome list a third column must be specified:
    3. the id of the space ("nt" or "cs" with no quotes).

To deploy the bfast.cgi script, use the following hierarchy in your web
directory:
	html/
	html/images/
	html/images/gradient.jpg
	html/images/error.jpg
	html/css/
	html/css/bfast.css
	cgi-bin/
	cgi-bin/bfast.cgi
You may need to change "bfast.cgi" to suit your needs.  For example, there
are some hard-coded paths and options in the "bfast.cgi" perl script, including:
	1. lines 17-19 (no need to modify if the hierarchy above is used).
	2. lines 668-674 specify where the tmp files will be stored. If you include
	a world-readable/world-writeable "tmp" directory in the above hierarchy, you
	should be ok.