table of contents
other versions
- stretch 1.2.3-11
biomaj(1) | USER COMMANDS | biomaj(1) |
NAME¶
biomaj - downloads and transform remote biological data banksSYNOPSIS¶
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 |