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)

version 1.2.0                                  September 14, 2011                                      biomaj(1)