Database Configuration
- Scott Saccone
MySQL
BioQ is designed to use free, open-source MySQL. We have tried implement BioQ with any other database managements systems at this time.
The BioQ MySQL User
A single user must be defined with certain privileges. This information is configured in the file BioqOptions.xml. The program init_mysql.php must be then be run to configure MySQL with these options. See the installation section for more information.
Databases
Must be installed | Database | Description |
|---|---|---|
YES | bioq_dbdoc | Primary documentation database. Used by bioq/dbdoc/*.php and dbdoc_util.pl. This can be found in the Subversion directory "databases" in the MySQL dump bioq_dbdoc.sql. Use load_dbdoc.sh to load this into MySQL. |
*YES | bioq_dbsnp_human_132 | Build 132 of the dbSNP human database. This can be downloaded from BioQ here. |
*YES | bioq_entrez_gene | Gene information from NCBI Entrez Gene. This is required when querying genes. This database can be found in the Subversion directory "databases" as the compressed file bioq_entrez_gene.sql.gz. |
*YES | bioq_hapmap_<version> | HapMap database for BioQ. At least one HapMap database is required when incorporating LD proxies into SNP queries. The default is to use the Public Release 28 database. This can be downloaded from BioQ here. |
NO | run_info_bioq | Contains the talbes run_info and threads. These are used to keep track of queries. This database is set in |
NO | tmp_bioq_<session_id> | Temporary BioQ databases. The prefix is defined in config.php. These databases are created automatically. |
*Some features will require this database.
Installing MySQL databases
In a Unix operating system where MySQL is installed and configured to be run without specifying a password (such as by using ~/.my.cnf), use commands like the following to load a MySQL database for use with BioQ:
mysqladmin create bioq_dbdoc gunzip -c bioq_dbdoc.sql.gz | mysql bioq_dbdoc