Using custom track database

Using the Custom Track Database

A new feature of the genome browser as of March 2007 is the ability to use a data base for custom tracks. Up to this date, custom track data has been kept in files in the /trash/ct/ directory. This article discusses the steps required to enable this function.

Summary configuration

• database loader binaries hgLoadBed, hgLoadWiggle and wigEncode are installed in /cgi-bin/loader/ - these are installed via the normal 'make cgi' in the source tree kent/src/hg/ directory.
• an empty customTrash database has been created on the MySQL host - create this manually once, the MySQL host name is a configuration item, the database name is not a configuration item
• temporary read-write data directory /data/tmp has been created with read/write/delete enabled for the Apache server effective user, this directory name is a configuration item
• configuration items are specified in /cgi-bin/hg.conf/ - this will turn on the function
• for command line access to the database, create a special ~/.hg.ct.conf to be used with the environment variable HGDB_CONF
• create a cron job to run a cleaner script to expire and remove older tables from the database - dbTrash command is used for this purpose

Host and database name

For performance and security considerations, the MySQL host for the custom track database can be a separate machine from the ordinary MySQL host that usually serves up the assembly databases or the hgcentral database. It is not required that the custom track database be on a separate MySQL server. The specification of the host machine is placed in the /cgi-bin/hg.conf file, for example a host machine called "ctdbhost":

customTracks.host=ctdbHost

The database name used on this host is fixed at customTrash which is a define in the source tree file hg/inc/customTrack.h

/cgi-bin/hg.conf configuration items

The following items must be specified in /cgi-bin/hg.conf to enable this function:

customTracks.host=ctdbhost
customTracks.user=ctdbuser
customTracks.password=ctdbpasswd
customTracks.useAll=yes

Establish this user account and password in MySQL with db and user privileges:

Select, Insert, Update, Delete, Create, Drop, Alter
for example with your MySQL root user account:
hgsql -hctdbhost -uroot -p -e "GRANT SELECT,INSERT,UPDATE,DELETE,CREATE,DROP,ALTER"
on customTrash TO ctdbuser@yourWebHost IDENTIFIED by 'ctdbpasswd';" mysql

Optionally, a temporary read-write directory used during database loading can be specified:

customTracks.tmpdir=/data/tmp

The default for this is /data/tmp and should be created with read/write/delete access for the Apache server effective user.