dc2a1aed940aee3152f6778d8e380b699792f426 hiram Thu May 23 15:09:51 2013 -0700 updating list of userApps in src/utils refs #9104 diff --git src/userApps/README src/userApps/README index 4a1b628..0b195a0 100644 --- src/userApps/README +++ src/userApps/README @@ -1,70 +1,70 @@ ========= 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 60 Mb of kent source code, - and constructs command binaries of approximately 120 Mb. + 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. ========= 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/ =========