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)