Query: biomaj
OS: debian
Section: 1
Format: Original Unix Latex Style Formatted with HTML and a Horizontal Scroll Bar
biomaj(1) USER COMMANDS biomaj(1)NAMEbiomaj - downloads and transform remote biological data banksSYNOPSISbiomaj [-h]DESCRIPTIONBioMAJ (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.INSTALLAt 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 USERA default admin user (admin) is created by the scripts. If using the biomaj-watcher, the default password (admin) MUST be changed immedi- atly via the watcher interface. If only biomaj core is used, password is useless. .PPUPGRADEIn 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 BANKSBy default, biomaj is configured (data.dir in global.properties) to write banks to /var/lib/biomaj.EXAMPLESUpdate a bank: biomaj --update genbank Show console biomaj --update genbank --console Show status: biomaj --statusEXIT STATUSbiomaj returns a zero exist status if it succeeds, it does not represent the bank update status.AUTHOROlivier Sallou (olivier.sallou (at) irisa.fr) Romaric Sabas (romaric.sabas (at) irisa.fr) version 1.2.0 September 14, 2011 biomaj(1)
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