###############
# Prerequisite
###############

A) Biomaj Workflow
   ---------------
   External tools used by Biomaj configured in /etc/biomaj/general.conf :

   GNU Tar 1.13 or higher ( http://www.gnu.org/software/tar/tar.html) 
   Gzip 1.3.3 or higher (http://www.gzip.org/) 
   Bzip2 0.9.0 or higher (http://sources.redhat.com/bzip2/) 
   Tar, Gzip, and Bzip2 are only needed if you need to extract files that use those compression formats. 


   The following list needs more attention :

   Java 1.6.x or higher ( http://java.sun.com/j2se/) 
   Ant 1.7.0 or higher ( http://ant.apache.org/) 

B) Post-processes
   --------------
            
   The post-processes are available in the conf/process directory
   of this package. Please note, that some packages may require some third-parity tools :

	- perl 5.8.x
	- ncbi blast  ftp.ncbi.nih.gov:/blast/executables/LATEST ==> formatdb & fastcmd programs
	- srs ==> 
	- readseq ==> http://iubio.bio.indiana.edu/soft/molbio/readseq/

###############
# Configuration
###############

See INSTALL file.

##############
# BmajWatcher
##############

BmajWatcher is a web interface for banks administration.
- With shipped tomcat server, open the following URL in your browser : http://localhost:8080/BmajWatcher/
- With a preinstalled tomcat server, copy the following files in your tomcat directory :
	* webapps/BmajWatcher.war
	* lib/biomaj.jar (symbolic link)
	* lib/GWT-2.0/
	* conf/Catalina/localhost/BmajWatcher.xml
	* conf/Catalina/localhost/BmajWatcher#logs.xml

################
# DATA MIGRATION
################

To migrate from xml statefiles (BioMAJ <= 1.0) to MySQL or HSQLDB a script is provided :
$BIOMAJ_ROOT/bin/import_statefiles.sh --dir someDir
$BIOMAJ_ROOT/bin/import_statefiles.sh --files bank1.xml bank2.xml ...
Configuration of MySQL server is left to the user.
The script to create the database is available at /usr/local/biomaj/sql/mysql.sql


###################
# USEFUL COMMANDS
###################

a) HELP :

    biomaj --help

b) Start update for alu bank :

    biomaj --update alu

c) Rebuild a bank (rerun the post-processes) :

    biomaj --rebuild alu

c) Status of the data repository

    biomaj --status

d) Status of a bank :

    biomaj --status <bank>

########################
# COMPLETE DOCUMENTATION 
#######################

BiomajWatcher specific doc : $BIOMAJ_ROOT/doc/BW_userguide.pdf
Biomaj general doc : $BIOMAJ_ROOT/doc/UsersGuide_BioMAJ_EN.pdf

