6a64112e35285dd6bc89131787bfa3e84d57ddc9
hiram
  Fri May 24 12:15:43 2013 -0700
updating userApps buildlist refs #9149
diff --git src/userApps/README src/userApps/README
index 0f29380..cbd51cd 100644
--- src/userApps/README
+++ src/userApps/README
@@ -1,130 +1,131 @@
 ========================================================================
 
 UCSC genome browser 'kent' bioinformatic utilities
 
   These are only the command line bioinformatic utilities
   from the kent source tree.  This is not the genome browser install.
   For the genome browser install, use the instructions from the source tree:
     http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=tree;f=src/product
 
 ========================================================================
 
 System Requirements:
 
 Linux/Ubuntu/CentOS/Unix/MacOSX operating 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 - http://dev.mysql.com/
 libpng runtime and development packages - http://www.libpng.org/
 libssl runtime and development packages - http://www.openssl.org/
 
 It is best to install these packages with your standard operating
 system package management tools.
     (see notes below about installing packages)
 
 ========================================================================
 
 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 small files.
 
 2. Build the 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 200 Mb.
+      kent source code, and constructs about 200 command binaries
+      of approximate size near 500 Mb.
    The resulting binaries are in ./userApps/bin/
 
    Note: there are no required shell environment settings as discussed
          in the genome browser build instructions.  In fact, this build
-         system will ignore any shell environment settings you may have
-         for the genome browser build environment.
+         system will ignore and override any shell environment settings
+         you may have for the genome browser build environment.
 
 3. Install utilities
 
    The binaries are built into ./userApps/bin/
    To install them in a global bin/ directory, copy them
    to a desired location, e.g.:
 
       sudo rsync -a -P ./userApps/bin/ /usr/local/bin/kentUtils/
 
    The destination bin/kentUtils/ should be its own unique directory
    to avoid overwriting same-named binaries in a standard bin/ directory.
 
    Users add '/usr/local/bin/kentUtils' to their shell PATH
    to access the commands.
 
 4. Update utilities
 
    cd userApps
    make update
 
    This runs a 'make clean' in the source tree, fetches all
    the source again, unpacks it to overlay the existing source tree,
    then runs a 'make utils' to rebuild everything.
 
 5. There are 'parasol' binaries built into ./userApps/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
 
 Depending upon the version of your Linux/Ubuntu/CentOS operating system,
 the specific version of packages you need may be different than this example.
 
 Please use your standard operating system package management
 install system (e.g. 'yum' on CentOS) to obtain correct versions of
 these packages for your specific operating system version.
 
 See also:
         https://help.ubuntu.com/8.04/serverguide/apt-get.html
         http://www.centos.org/docs/5/html/yum/
 
 ========================================================================
 
 Known Problems:
 
 1. These procedures will not work as-is on sparc or alpha machines or
    with the Sun Solaris operating system.
 
 ========================================================================