Downloads and transform remote biological data banks
biomaj [-h]
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.
-h
display the list of commands.
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.
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
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.
By default, biomaj is configured (data.dir in global.properties) to write banks to /var/lib/biomaj.
Update a bank:
biomaj --update genbank
Show console
biomaj --update genbank --console
Show status:
biomaj --status
biomaj returns a zero exist status if it succeeds, it does not represent the bank update status.
Olivier Sallou (olivier.sallou (at) irisa.fr) Romaric Sabas (romaric.sabas (at) irisa.fr)