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

diff --git src/hg/utils/automation/aws/hubStart.txt src/hg/utils/automation/aws/hubStart.txt
index 913030d2687..d2c8e785ad1 100644
--- src/hg/utils/automation/aws/hubStart.txt
+++ src/hg/utils/automation/aws/hubStart.txt
@@ -69,31 +69,31 @@
   printf "export AWS_SECRET_ACCESS_KEY=AWS_SecretKey\n" >> "${homeDir}/.bashrc"
   printf "instId: %s, availZone: %s, region: %s\n" "${instanceId}" "${availZone}" "${region}" >> "${logFile}"
   printf "set background=dark\n" >> "${homeDir}/.vimrc"
 
   # install the wget command right away so the wgets can get done
   yum -y install wget >> "${logFile}" 2>&1
   # and the kent command line utilities into /data/bin/
   rsync -a --stats rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/ /data/bin/ >> "${logFile}" 2>&1
   # initParasol script to manage start/stop of parasol system
   wget -qO /data/parasol/initParasol 'http://genomewiki.ucsc.edu/images/4/4f/InitParasol.sh.txt' >> "${logFile}" 2>&1
   chmod 755 /data/parasol/initParasol
   # script in nodeInfo to be used by the nodes to report themselves
   wget -qO /data/parasol/nodeInfo/nodeReport.sh 'http://genomewiki.ucsc.edu/images/e/e3/NodeReport.sh.txt' >> "${logFile}" 2>&1
   chmod 755 /data/parasol/nodeInfo/nodeReport.sh
   # bedSingleCover.pl for use in running featureBits like measurements
-  wget -P /data/scripts 'https://genome-source.gi.ucsc.edu/gitlist/kent.git/raw/master/src/utils/bedSingleCover.pl' >> "${logFile}" 2>&1
+  wget -P /data/scripts 'https://github.com/ucscGenomeBrowser/kent/raw/master/src/utils/bedSingleCover.pl' >> "${logFile}" 2>&1
   chmod +x /data/scripts/bedSingleCover.pl
   chown -R ${nativeUser}:${nativeUser} /data "${homeDir}/bin" "${homeDir}/.vimrc"
 
   # ec2-user HOME/bin/attachVolume.sh used to attach extra data volume
   wget -qO "${homeDir}/bin/attachVolume.sh"  'http://genomewiki.ucsc.edu/images/2/2c/AwsAttachVolume.sh.txt' >> "${logFile}" 2>&1
   chmod 755 "${homeDir}/bin/attachVolume.sh"
   chown ${nativeUser}:${nativeUser} "${homeDir}/bin/attachVolume.sh"
   chown ${nativeUser}:${nativeUser} "/genomes"
 
   # and now can start the rest of yum installs, these take a while
   # useful to have the 'host' command, 'traceroute' and nmap ('nc')
   # to investigate the network, wget for transfers, and git for kent source tree
   # the git-all installs 87 packages, including perl, tcsh for the csh shell,
   # screen for terminal management, vim for editing convenience, bc for math
   yum -y update >> "${logFile}" 2>&1
@@ -104,31 +104,31 @@
   yum -y install python-pip gcc gcc-c++ zlib-devel python-devel tkinter libpng12 strace >> "${logFile}" 2>&1
   pip install --ignore-installed pytabix pandas twobitreader scipy matplotlib numpy >> "${logFile}" 2>&1
   pip install scikit-learn==0.16.1 Biopython xlwt >> "${logFile}" 2>&1
 
   # these systemctl commands may not be necessary
   # the package installs may have already performed these initalizations
   systemctl enable rpcbind >> "${logFile}" 2>&1
   systemctl enable nfs-server >> "${logFile}" 2>&1
   systemctl start rpcbind >> "${logFile}" 2>&1
   systemctl start nfs-server >> "${logFile}" 2>&1
   systemctl start nfs-lock >> "${logFile}" 2>&1
   systemctl start nfs-idmap >> "${logFile}" 2>&1
 
   # this business needs to be improved to be a single rsync from
   # a download directory.
-  git archive --format=tar --remote=git://genome-source.soe.ucsc.edu/kent.git \
+  git archive --format=tar --remote=https://github.com/ucscGenomeBrowser/kent.git \
       --prefix=kent/ HEAD src/hg/utils/automation \
         | tar vxf - -C /data/scripts --strip-components=5 \
       --exclude='kent/src/hg/utils/automation/incidentDb' \
       --exclude='kent/src/hg/utils/automation/configFiles' \
       --exclude='kent/src/hg/utils/automation/ensGene' \
       --exclude='kent/src/hg/utils/automation/genbank' \
       --exclude='kent/src/hg/utils/automation/lastz_D' \
       --exclude='kent/src/hg/utils/automation/openStack' >> "${logFile}" 2>&1
 
   chown -R ${nativeUser}:${nativeUser} /data/scripts >> "${logFile}" 2>&1
 
   # setup NFS exports
   export localIp=`curl http://169.254.169.254/latest/meta-data/local-ipv4`
   export privateIp=`ifconfig -a | grep broadcast | head -1 | awk '{print $2}'`
   export subNet=`ifconfig -a | grep broadcast | head -1 | awk '{print $2}' | awk -F'.' '{printf "%s.%s.0.0", $1,$2}'`