Using custom track database: Difference between revisions
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A new feature of the genome browser as of March 2007 is the ability | 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 | 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. | data has been kept in files in the <em>/trash/ct/</em> directory. | ||
This article discusses the steps required to enable this function. | |||
==Summary configuration== | |||
<ul> | |||
<li>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.</li> | |||
<li>an empty customTrash database has been created on the MySQL host - create this manually once</li> | |||
<li>configuration items are specified in /cgi-bin/hg.conf/ - this will turn on the function</li> | |||
<li>for command line access to the database, create a special ~/.hg.ct.conf to be used with the environment variable HGDB_CONF</li> | |||
<li>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</li> | |||
</ul> | |||
==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 <em>/cgi-bin/hg.conf</em> file, for | |||
example a host machine called <em>"ctdbhost":</em> | |||
<pre> | |||
customTracks.host=ctdbHost | |||
</pre> | |||
The database name used on this host is fixed at <em>customTrash</em> | |||
Revision as of 19:15, 2 March 2007
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
- 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
