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Shell Programming and Scripting
Test an url
Post 58236 by Olivier on Tuesday 16th of November 2004 10:05:17 AM
11-16-2004
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LEARN ABOUT DEBIAN
biomaj
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 immedi- atly 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) version 1.2.0 September 14, 2011 biomaj(1)