5adcf6bc2904690de7b7b30a83ec8a7a0996abe9
galt
  Tue Aug 21 00:01:25 2018 -0700
changing cse subdomain to soe

diff --git src/userApps/README src/userApps/README
index 54feecd..af4cea4 100644
--- src/userApps/README
+++ src/userApps/README
@@ -5,76 +5,76 @@
   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, see the mirror instructions:
     http://genome.ucsc.edu/goldenPath/help/mirror.html
 
 ========================================================================
 Pre-compiled binaries available:
 
 These binaries built at UCSC may already work in your linux/Mac
 environment.  Please access via rsync:
 
   rsync -a -P rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/ ./
   rsync -a -P rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/macOSX.x86_64/ ./
 
 Or via HTTP:
-  http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
-  http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/
+  http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/
+  http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/
 
 Or via FTP:
-  ftp://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
-  ftp://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/
+  ftp://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/
+  ftp://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/
 
 Note: access via HTTP or FTP does not copy with the 'execute' bits on,
 to enable execute bits on files in a directory:  chmod +x ./*
 
 ========================================================================
 
 System Requirements:
 
 Linux/Ubuntu/CentOS/Unix/MacOSX operating system
 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/
 libuuid-devel - https://rpmfind.net/linux/rpm2html/search.php?query=libuuid-devel
 
 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:
 
    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
+     ftp://hgdownload.soe.ucsc.edu/apache/htdocs/admin/exe/userApps.src.tgz
+     http://hgdownload.soe.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 \
+      --remote=git://genome-source.soe.ucsc.edu/kent.git \
       beta src/userApps > userApps.zip
    unzip -d userApps -j userApps.zip
    cd userApps
    make fetchSource
 
 2. Build the utilities:
 
    cd userApps
    make
 
    This build fetches (with git) approximately 200 Mb/7,800 files of
       kent source code, and constructs about 223 command binaries
       of approximate size near 600 Mb.
    The resulting binaries are in ./userApps/bin/
 
@@ -105,62 +105,62 @@
    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.html
+     http://genecats.soe.ucsc.edu/eng/parasol.html
    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
 
 Please note: kent commands use the special keywords:
    'stdin', 'stdout' and 'stderr' in place of input or output file name
    arguments.  This is unlike the default unix command line behavior
    of having 'stdin' and 'stdout' as default input and output arguments
    without mention.
 
 ========================================================================
 
 MySQL database access:
 
 Many of the commands can use the UCSC public MySQL server, or
 your own local MySQL server with UCSC data formats.  Add these three
 lines to a file in your HOME directory called '.hg.conf' and set
 its permissions to: 'chmod 600 .hg.conf'
 
-    db.host=genome-mysql.cse.ucsc.edu
+    db.host=genome-mysql.soe.ucsc.edu
     db.user=genomep
     db.password=password
     central.db=hgcentral
 
 This '.hg.conf' file is used by the kent commands to determine the
 MySQL host and user/password to the database.  For your local MySQL
 installation, use your host name and your read-only user/password names.
 
 ========================================================================
 
 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/