58426dc61940e28010f76b6ad9a59c22d4b6fae2 hiram Thu May 23 16:13:23 2013 -0700 adding parasol to the userApps build refs #9104 diff --git src/userApps/README src/userApps/README index 0b195a0..ba7c13c 100644 --- src/userApps/README +++ src/userApps/README @@ -32,30 +32,46 @@ This build fetches (with git) approximately 200 Mb/7,800 files of kent source code, and constructs command binaries of approximately 120 Mb. 3. Install utilities The binaries are built into userApps/bin/ To install them in a global bin/ directory, copy them to desired location: sudo rsync -a -P bin/ /usr/local/bin/userApps/ The destination bin/userApps/ should be its own unique directory to avoid overwriting same-named binaries in a standard bin/ directory. Users add '/usr/local/bin/userApps' to their shell PATH to access the commands. + +4. There are 'parasol' binaries built in kent/src/parasol/bin/ + Use these binaries to set up a job control system on a compute cluster + or large machine with many CPU cores. See also: + http://genecats.cse.ucsc.edu/eng/parasol.htm + for more information. The usage messages from each command will help + with the setup. + +========= + +Documentation: + +Each 'kent' command contains its own documentation. Simply run the +commands without any arguments to see the usage message for operating +instructions. + ========= 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 \