62b1428915cc2c8b9acbf46a86c1248833257efe
mspeir
  Mon Nov 17 18:50:32 2025 -0800
changing rest of genome-source references to github, refs #34485

diff --git src/product/scripts/kentSrcUpdate.sh src/product/scripts/kentSrcUpdate.sh
index ccaea0501a7..91b7d54e5a2 100755
--- src/product/scripts/kentSrcUpdate.sh
+++ src/product/scripts/kentSrcUpdate.sh
@@ -1,91 +1,91 @@
 #!/bin/bash
 #
 #	$Id: kentSrcUpdate.sh,v 1.1 2010/03/18 18:40:12 hiram Exp $
 #
 usage() {
     echo "usage: kentSrcUpdate.sh <browserEnvironment.txt>" 1>&2
     echo "  the browserEnvironment.txt file contains definitions of how" 1>&2
     echo "  these scripts behave in your local environment." 1>&2
     echo "There should be an example template to start with in the" 1>&2
     echo "directory with these scripts." 1>&2
     exit 255
 }
 
 export includeFile=$1
 if [ "X${includeFile}Y" = "XY" ]; then
     usage
 fi
 
 if [ -f "${includeFile}" ]; then
     . "${includeFile}"
 else
     echo "ERROR: kentSrcUpdate.sh: can not find ${includeFile}" 1>&2
     usage
 fi
 
 export errCount=0
 if [ ! -d "${BROWSERHOME}" ]; then
     echo "ERROR: BROWSERHOME directory does not exist: ${BROWSERHOME}" 1>&2
     errCount=`echo $errCount | awk '{print $1+1}'`
 fi
 if [ ! -d "${CGI_BIN}" ]; then
     echo "ERROR: CGI_BIN directory does not exist: ${CGI_BIN}" 1>&2
     errCount=`echo $errCount | awk '{print $1+1}'`
 fi
 
 if [ $errCount -gt 0 ]; then
     echo "ERROR: check on the existence of the mentioned directories" 1>&2
     exit 255
 fi
 
 # this umask will allow all group members to write on files of other
 # group members
 umask 002
 
 mkdir -p "${kentSrc}"
 
 #	clean the source tree before updating it, this will lead
 #	to a cleaner report from git pull
 if [ -d "${kentSrc}/src" ]; then
     cd "${kentSrc}/src"
     make clean > /dev/null 2> /dev/null
     rm -f tags daily.log utils.log blatSuite.log
 else
     #	first time, needs to establish the source tree
     cd "${kentSrc}"
     cd ..
     rmdir kent
-    time git clone git://genome-source.soe.ucsc.edu/kent.git
+    time git clone https://github.com/ucscGenomeBrowser/kent.git
     cd kent
     git checkout -t -b beta origin/beta
     cd ..
 fi
 
 # not necessary, but this is where it is happening
 cd "${kentSrc}"
 
 testHere=`pwd`
 if [ "X${testHere}Y" != "X${kentSrc}Y" ]; then
     echo "ERROR: kentSrcUpdate.sh failed to chdir to ${kentSrc}" 1>&2
     exit 255;
 fi
 echo "git update report summary is in email to ${LOGNAME}" 1>&2
 /usr/bin/git pull 2>&1 | mail -s 'GIT update report kent' "${LOGNAME}"
 
 #	And then, let's build it all
 cd "${kentSrc}/src"
 testHere=`pwd`
 if [ "X${testHere}Y" != "X${kentSrc}/srcY" ]; then
     echo "ERROR: kentSrcUpdate.sh failed to chdir to ${kentSrc}/src" 1>&2
     exit 255;
 fi
 MAKE="make -j 4" make -j 4 cgi-alpha > daily.log 2>&1
 #	If there are any errors, they will come via separate email from cron
 egrep -y "erro|warn" daily.log | grep -v "\-Werror" | \
 	egrep -v "disabling jobserver mode|-o gbWarn.o |-o hgTracks |gbExtFile.o gbWarn.o gbMiscDiff.o"
 make tags-all > /dev/null 2> /dev/null
 # assuming $HOME/bin/$MACHTYPE is a symlink to /genome/browser/bin/$MACHTYPE
 #	then all the utilities will end up there
 make utils > utils.log 2>&1
 make blatSuite > blatSuite.log 2>&1
 # do not want to check for errors in these utils.log blat