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 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

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)