59c426e232a372f56cfe9a379d3b44e6a5d50895
hiram
  Thu May 23 09:17:02 2013 -0700
begin structure to fetch and build the user apps at an external location
diff --git src/userApps/README src/userApps/README
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+=========
+
+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 -q userApps.zip
+
+   Creates the directory ./userApps/
+
+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.
+
+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/
+
+=========