Downloading Data using MySQL

We have two MySQL databases for public access:

• genome-mysql.soe.ucsc.edu (located on the US west coast)
• genome-euro-mysql.soe.ucsc.edu (located in Europe)

These servers allow MySQL access to the same set of data currently available on our public Genome Browser site. The data are synchronized weekly with the main databases on our public site. During synchronization, the MySQL server can be intermittently out of sync with the main website for a short period of time. The weekly synchronization takes place on Monday mornings from 4:00 am to 9:00 am Pacific Time (GMT -7:00 in summer, GMT -8:00 in winter).

Connecting

You must have MySQL client libraries installed on your computer. We recommend using the most current version of the v5.0 MySQL clients.

You can connect to the US MySQL server using the command:

mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -P 3306

Or the European MySQl server with this command:

mysql --user=genome --host=genome-euro-mysql.soe.ucsc.edu -A -P 3306

The -A flag is optional but is recommended for speed.

Once connected to the database, you may use a wide range of MySQL commands to query the database.

Conditions of use

• Avoid excessive or heavy queries that may impact the server performance. Inappropriate query use will result in a restriction of access. If you plan to execute a query that you think may be excessive, contact UCSC first to avoid the possibility of having your access blocked.
• Bot access and excessive program-driven use are not permitted.
• Attachments by local mirror sites are prohibited.

Using the MySQL server with our utilities

The MySQL database can also be used by the numerous utilities in the Genome Browser source tree. Some of these utilities require a password, so you will need to add the following specifications to your $HOME/.hg.conf file (remember to chmod your .hg.conf file to 600 permissions) if you would like to access the US public MySQL server:

#US MySQL server
db.host=genome-mysql.soe.ucsc.edu
db.user=genomep
db.password=password
central.db=hgcentral
central.host=genome-mysql.soe.ucsc.edu
central.user=genomep
central.password=password
gbdbLoc1=http://hgdownload.soe.ucsc.edu/gbdb/
forceTwoBit=on

Or these lines if you'd like to access the European MySQL server:

#European MySQL server
db.host=genome-euro-mysql.soe.ucsc.edu
db.user=genomep
db.password=password
central.db=hgcentral
central.host=genome-euro-mysql.soe.ucsc.edu
central.user=genomep
central.password=password
gbdbLoc1=http://hgdownload.soe.ucsc.edu/gbdb/
forceTwoBit=on

The db.* and central.* settings tell our utilities how to connect to the public MySQL server. The gbdbLoc1 setting tells our utilities where to find data files. The forceTwoBit setting is necessary for utilities that retrieve genomic sequence.

If you have set up your .hg.conf file as above, you can use the hgsql utility, available from our downloads server in the Utilities section, to access the public MySQL server. The benefit of using the hgsql command is that you don't have to include the username or password as part of your command. You only need to specify the host:

hgsql -h genome-mysql.soe.ucsc.edu

If you prefer a graphical user interface (GUI) to the UCSC database tables, use the Table Browser.

System problems should be reported to genome-www@soe.ucsc.edu. Send questions regarding the database contents or queries to genome@soe.ucsc.edu. Messages sent to this address will be posted to the moderated genome mailing list, which is archived on a SEARCHABLE, PUBLIC Google Groups forum.