debian man page for biomaj

biomaj(1)							   USER COMMANDS							 biomaj(1)

NAME
       biomaj - downloads and transform remote biological data banks

SYNOPSIS
       biomaj [-h]

DESCRIPTION
       BioMAJ (BIOlogie Mise A Jour) is a workflow engine dedicated
	to data synchronization and processing.The Software automates
	the update cycle and the supervision of the locally mirrored
	databank repository.  User must have roots rights to run biomaj.

OPTIONS
       -h     display the list of commands.

INSTALL
       At  installation, BioMAJ requires a database to run (MySQL), installer should first create a database (biomaj_log) and a database user (the
       one used at installation setup).
	The database configuration for biomaj can be set or modified in /etc/biomaj/db_properties/global.properties.

       In the install fails due to a SQL error, the install script must be manually run to create/upgrade the database:

       perl /usr/share/biomaj/sql/migration/update.pl

       The script will create/upgrade the database and update the configuration files.

ADMIN USER
       A default admin user (admin) is created by the scripts.	If using the biomaj-watcher, the default password (admin) MUST be changed  immedi-
       atly via the watcher interface.

       If only biomaj core is used, password is useless.
	.PP

UPGRADE
	In the case of a package upgrade, if properly configured, the migration scripts will be ran automatically at install.
	It is possible to run manually the script:
	.B See perl /usr/share/biomaj/sql/migration/update.pl -h
	for usage.

DATA BANKS
       By default, biomaj is configured (data.dir in global.properties) to write banks to /var/lib/biomaj.

EXAMPLES
       Update a bank:
	      biomaj --update genbank

       Show console
	      biomaj --update genbank --console

       Show status:
	      biomaj --status

EXIT STATUS
       biomaj returns a zero exist status if it succeeds, it does not represent the bank update status.

AUTHOR
       Olivier Sallou (olivier.sallou (at) irisa.fr) Romaric Sabas (romaric.sabas (at) irisa.fr)

version 1.2.0							September 14, 2011							 biomaj(1)