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 immediatly 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

AUTHOR

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