b70c24dfd5fa26cf2eded5becef8abd7ae5f2990 hiram Tue Aug 6 11:24:49 2013 -0700 add note about MySQL access refs #9149 diff --git src/userApps/README src/userApps/README index b49bb60..2e7a46a 100644 --- src/userApps/README +++ src/userApps/README @@ -116,30 +116,47 @@ ======================================================================== Documentation: Each 'kent' command contains its own documentation. Simply run the commands without any arguments to see the usage message for operating instructions. When the utilities are built here, their usage messages have been collected together in one file: kentUtils.Documentation.txt ======================================================================== +MySQL database access: + +Many of the commands can use the UCSC public MySQL server, or +your own local MySQL server with UCSC data formats. Add these three +lines to a file in your HOME directory called '.hg.conf' and set +its permissions to: 'chmod 600 .hg.conf' + + db.host=genome-mysql.cse.ucsc.edu + db.user=genomep + db.password=password + +This '.hg.conf' file is used by the kent commands to determine the +MySQL host and user/password to the database. For your local MySQL +installation, use your host name and your read-only user/password names. + +======================================================================== + Installing required packages: On a MacOS system, you will need the XCode system installed: https://developer.apple.com/xcode/ And the Mac Ports install system: http://www.macports.org/ With the Mac ports and XCode systems installed, you can install the additional packages required (and helpful): sudo port install git-core gnutls rsync libpng mysql55 openssl curl wget On a typical Linux system, for example Ubuntu, use the apt-get command to install additional packages: sudo apt-get install git libssl-dev openssl mysql-client-5.1 \