b16a503329f7153bae74daea4626f24ac2e70363 hiram Thu May 23 16:37:11 2013 -0700 update comment about resulting size of binaries refs #9104 diff --git src/userApps/README src/userApps/README index 7d32f26..7f36e9c 100644 --- src/userApps/README +++ src/userApps/README @@ -1,90 +1,90 @@ ========= UCSC genome browser 'kent' bioinformatic utilities ========= System Requirements: (see notes below about installing packages) Linux/Unix/MacOSX system 'git' source code management: http://git-scm.com/downloads gnu gcc - C code development system - http://www.gnu.org/software/gcc/ gnu make - http://www.gnu.org/software/make/ MySQL development system and libraries libpng libssl ========= 1. Fetch the userApps directory from the kent source: git archive --format=zip -9 \ --remote=git://genome-source.cse.ucsc.edu/kent.git \ HEAD src/userApps > userApps.zip unzip -d userApps -j userApps.zip Creates the directory: ./userApps/ with several files. 2. Build utilities: cd userApps make This build fetches (with git) approximately 200 Mb/7,800 files of - kent source code, and constructs command binaries of approximately 120 Mb. + kent source code, and constructs command binaries of approximately 200 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. When the utilities are built here, their usage messages have been collected together in one file: kentUtils.Documentation.txt ========= 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 \ mysql-client-core-5.1 Or appropriate system management install software (e.g. 'yum' on CentOS) See also: https://help.ubuntu.com/8.04/serverguide/apt-get.html http://www.centos.org/docs/5/html/yum/ =========