3ccf49931df17a0763b6ffea00823eb60d15cf95
hiram
  Fri Jun 7 09:29:16 2013 -0700
indicate an alternative to using git refs #9149
diff --git src/userApps/README src/userApps/README
index 20b64a1..5731a93 100644
--- src/userApps/README
+++ src/userApps/README
@@ -1,83 +1,103 @@
 ========================================================================
 
 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/
 
+Optional:
+'git' source code management: http://git-scm.com/downloads
+
 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:
+1. Fetch the userApps directory:
+
+   Alternative to 'git' command, a gzipped tar file is available
+   with all the source, via FTP or HTTP:
+     ftp://hgdownload.cse.ucsc.edu/apache/htdocs/admin/exe/userApps.src.tgz
+     http://hgdownload.cse.ucsc.edu/admin/exe/userApps.src.tgz
+
+   Unpacking that file (tar xvzf userApps.src.tgz)
+   creates a directory: ./userApps/
+   with all the source.  Proceed to step 2 to build this directory.
+
+   Using 'git' to fetch the source, creates a directory ./userApps/
 
    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.
+   cd userApps
+   make fetchSource
 
 2. Build the utilities:
 
    cd userApps
-   make fetchSource
    make
 
    This build fetches (with git) approximately 200 Mb/7,800 files of
-      kent source code, and constructs about 200 command binaries
-      of approximate size near 500 Mb.
+      kent source code, and constructs about 223 command binaries
+      of approximate size near 600 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 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
 
+   This procedure expects the 'git' command to be available.
+   Without the 'git' command, run a 'make clean' to clean up the
+   existing source tree, then repeat the fetch and unpack of the
+   userApps.src.tgz file as mentioned in step 1.
+
+   With the 'git' command available, the 'make update' will refresh
+   the source tree and rebuild:
+
    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.
 
 ========================================================================