---
name: "biomaj"
section: "1"
platform: "linux"
package: "biomaj"
version: "1.2.3-11"
release: "Debian 9 (Stretch)"
platforms: ["linux"]
url: "https://new.carta.tech/biomaj"
---

# biomaj(1)

downloads and transform remote biological data banks

## 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)