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biomaj - downloads and transform remote biological data banks

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 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)
September 14, 2011 version 1.2.0