c1fdd27f529b1e579d230e8f66a38b54baa605e2 ccpowell Mon Jul 8 15:55:31 2019 -0700 Changing MySQL to MariaDB in htdocs, #23597 diff --git src/hg/htdocs/goldenPath/help/mysql.html src/hg/htdocs/goldenPath/help/mysql.html index d82ee32..28ce449 100755 --- src/hg/htdocs/goldenPath/help/mysql.html +++ src/hg/htdocs/goldenPath/help/mysql.html @@ -1,111 +1,111 @@

Downloading Data using MySQL

-We have two MySQL databases for public access: +We have two MariaDB 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 +These servers allow MariaDB 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 +During synchronization, the MariaDB 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:

+You can connect to the US MariaDB server using the command:

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

Or the European MySQl server with this command:

Or the European MariaDB 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

Using the MariaDB server with our utilities

-The MySQL database can also be used by the numerous utilities in the +The MariaDB 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
+permissions) if you would like to access the US public MariaDB server:
+#US MariaDB 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:
+Or these lines if you'd like to access the European MariaDB 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 db.* and central.* settings tell our utilities how to connect to the public MariaDB 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
+to access the public MariaDB 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.