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

diff --git src/browserbox/root/updateBrowser.sh src/browserbox/root/updateBrowser.sh
index 53beca9..b8fe897 100755
--- src/browserbox/root/updateBrowser.sh
+++ src/browserbox/root/updateBrowser.sh
@@ -32,34 +32,34 @@
 # In case something goes wrong it continues, this is intentional to 
 # avoid a virtual machine that can not update itself anymore
 
 # rsync options:
 # l = preserve symlinks
 # t = preserve time
 # r = recurse
 # z = compress
 # v = verbose
 # h = human readable
 # u = skip if file is newer on receiver
 # We are not using the -z option anymore because it may cause
 # CPU overload on hgdownload
 RSYNCOPTS="-ltrvh"
 # rsync server for CGIs and html files
-RSYNCSRC="rsync://hgdownload.cse.ucsc.edu"
+RSYNCSRC="rsync://hgdownload.soe.ucsc.edu"
 RSYNCCGIBIN=cgi-bin
 RSYNCHTDOCS=htdocs
-UPDATEFLAG=http://hgdownload.cse.ucsc.edu/gbib/lastUpdate
+UPDATEFLAG=http://hgdownload.soe.ucsc.edu/gbib/lastUpdate
 LOGFILE=/var/log/gbibUpdates.log
 DEBUG=0
 if [[ "$#" -ne 0 ]]; then
     DEBUG=1
 fi
 
 # function to echo only if run with some arguments
 function echoDebug {
    if [[ DEBUG -eq "1" ]]; then
      echo $*
    fi
 } 
 
 # make sure that apt-get never opens an interactive dialog
 export DEBIAN_FRONTEND=noninteractive 
@@ -302,31 +302,31 @@
     rsync $RSYNCAPACHE $user@hgwdev.soe.ucsc.edu:/usr/local/apache/cgi-bin${cgiExt}/ /usr/local/apache/cgi-bin/
 
     PUSHLOC=$user@hgwdev.soe.ucsc.edu:/usr/local/apache/htdocs/gbib/push/
 
 # normal public updates from hgdownload are easier, not many excludes necessary
 else
     # update CGIs
     echo - Updating CGIs...
     rsync --delete -u $RSYNCOPTS $RSYNCSRC/$RSYNCCGIBIN /usr/local/apache/cgi-bin/ --exclude=hg.conf --exclude=hg.conf.local --exclude edw* --exclude *private --exclude hgNearData --exclude visiGeneData --exclude Neandertal 
 
     echo - Updating HTML files...
     # not using -u because we had a case with a 0-byte html page that was 
     # not updated anymore in #18337
     rsync --delete $RSYNCOPTS $RSYNCSRC/$RSYNCHTDOCS/ /usr/local/apache/htdocs/ --include **/customTracks/*.html --exclude ENCODE/ --exclude *.bam --exclude *.bb --exclude */*.bw --exclude */*.gz --exclude favicon.ico --exclude folders --exclude ancestors --exclude admin --exclude goldenPath/customTracks --exclude images/mammalPsg --exclude style/gbib.css --exclude images/title.jpg --exclude images/homeIconSprite.png --exclude goldenPath/**.pdf --exclude training
 
-    PUSHLOC=hgdownload.cse.ucsc.edu::gbib/push/
+    PUSHLOC=hgdownload.soe.ucsc.edu::gbib/push/
 fi
 
 chown -R www-data.www-data /usr/local/apache/cgi-bin/*
 chown -R www-data.www-data /usr/local/apache/htdocs/
 chmod -R a+r /usr/local/apache/htdocs
 
 # June 2017: add a basic set of hg38 files to the GBIB
 # This will add 1.2 GB to the size of the virtual disc but hg38
 # is the default genome so probably should be included
 # Touching the files once is enough. Rsync will download them.
 mkdir -p /data/gbdb/hg38
 mkdir -p /data/gbdb/hg38/targetDb/
 mkdir -p /data/gbdb/hg38/html/
 mkdir -p /data/mysql/hg38
 
@@ -338,31 +338,31 @@
 # MySQL tables
 for i in chromInfo cytoBand cytoBandIdeo ensemblLift extFile grp gtexGene gtexGeneModel hgFindSpec kgColor kgXref knownCanonical knownGene knownToTag ncbiRefSeq ncbiRefSeqCurated ncbiRefSeqLink ncbiRefSeqOther ncbiRefSeqPredicted ncbiRefSeqPsl refGene tableList trackDb ucscToEnsembl ucscToINSDC xenoRefGene; do
    touch /data/mysql/hg38/$i.MYD;
    touch /data/mysql/hg38/$i.MYI;
    touch /data/mysql/hg38/$i.frm;
 done
 
 # adding tables that are required for gtex, which is now a default track, #19587
 touch /data/mysql/hgFixed/gtexInfo.{MYI,MYD,frm}
 touch /data/mysql/hgFixed/gtexTissue.{MYI,MYD,frm}
 
 # -- END JUNE 2017
 
 if [ "$1" != "hgwdev" ] ; then
   echo - Updating GBDB files...
-  rsync $RSYNCOPTS --existing rsync://hgdownload.cse.ucsc.edu/gbdb/ /data/gbdb/
+  rsync $RSYNCOPTS --existing rsync://hgdownload.soe.ucsc.edu/gbdb/ /data/gbdb/
   chown -R www-data.www-data /data/gbdb/
 fi
 
 echo - Pulling other files
 # make sure we never overwrite the hg.conf.local file
 rsync $RSYNCOPTS $PUSHLOC / --exclude=hg.conf.local
 
 # July 2016: add the cram fetcher to root's crontab 
 # this has to be done after the PUSHLOC directory has been copied over
 if grep -q fetchCramReference /var/spool/cron/crontabs/root; then
         true
    else
        crontab -l | awk '{print} END {print "\n# handle CRAM auto reference download\n*/1 * * * * /root/fetchCramReference.sh /data/cramCache/pending /data/cramCache/ /data/cramCache/error/\n"}' | crontab -   
 fi
 # also create the directories for the cram files
@@ -389,36 +389,36 @@
 else
     echo Allowing LOAD DATA in MySQL and restart MySQL
     sed -i '/\[mysqld\]/a secure-file-priv = ""' /etc/mysql/my.cnf
     service mysql restart
 fi
 
 # we can now remove the old tables
 rm -f /data/mysql/hg19/refSeqStatus*
 
 if [ "$1" != "hgwdev" ] ; then
   echo updating MYSQL files - browser will not work during the MYSQL update
   # inspired by http://forums.mysql.com/read.php?35,45577,47063#msg-47063
   # it doesn't work if I use two mysql invocations, as 'flush tables with read lock'
   # is only valid as long as the session is open
   # so I use the SYSTEM command
-  echo "FLUSH TABLES WITH READ LOCK; SYSTEM rsync $RSYNCOPTS --existing rsync://hgdownload.cse.ucsc.edu/mysql/ /data/mysql/; SYSTEM chown -R mysql.mysql /data/mysql/; UNLOCK TABLES;" | mysql
+  echo "FLUSH TABLES WITH READ LOCK; SYSTEM rsync $RSYNCOPTS --existing rsync://hgdownload.soe.ucsc.edu/mysql/ /data/mysql/; SYSTEM chown -R mysql.mysql /data/mysql/; UNLOCK TABLES;" | mysql
   
   echo updating hgcentral database, make sure to always overwrite
-  echo "FLUSH TABLES WITH READ LOCK; SYSTEM rsync -vrz --existing rsync://hgdownload.cse.ucsc.edu/mysql/hgcentral/ /data/mysql/hgcentral/; SYSTEM chown -R mysql.mysql /data/mysql/hgcentral; UNLOCK TABLES;" | mysql
+  echo "FLUSH TABLES WITH READ LOCK; SYSTEM rsync -vrz --existing rsync://hgdownload.soe.ucsc.edu/mysql/hgcentral/ /data/mysql/hgcentral/; SYSTEM chown -R mysql.mysql /data/mysql/hgcentral; UNLOCK TABLES;" | mysql
   # update blat servers
-  mysql hgcentral -e 'UPDATE blatServers SET host=CONCAT(host,".cse.ucsc.edu") WHERE host not like "%ucsc.edu"'
+  mysql hgcentral -e 'UPDATE blatServers SET host=CONCAT(host,".soe.ucsc.edu") WHERE host not like "%ucsc.edu"'
   # the box does not officially support the HAL right now, remove the ecoli hubs
   mysql hgcentral -e 'delete from hubPublic where hubUrl like "%nknguyen%"'
 fi
 
 echo - Adapting the menu 
 cp /usr/local/apache/htdocs/inc/globalNavBar.inc /tmp/navbar.inc
 # remove mirrors and downloads menu
 sed -i '/<li class="menuparent" id="mirrors">/,/^<\/li>$/d' /tmp/navbar.inc 
 sed -i '/<li class="menuparent" id="downloads">/,/^<\/li>$/d' /tmp/navbar.inc 
 # adding the link to the mirror tracks tool
 sed -i '/hgLiftOver/a <li><a href="../cgi-bin/hgMirror">Mirror tracks</a></li>' /tmp/navbar.inc
 # add a link to the gbib shared data folder
 sed -i '/Track Hubs/a <li><a target="_blank" href="http:\/\/127.0.0.1:1234\/folders\/">GBiB Shared Data Folder<\/a><\/li>' /tmp/navbar.inc
 # adding a link to the GBIB help pages
 sed -i '/genomewiki/a <li><a href="../goldenPath/help/gbib.html">Help on GBiB</a></li>' /tmp/navbar.inc
@@ -474,26 +474,26 @@
    echo Creating /usr/local/apache/cgi-bin/hg.conf.local
    echo allowHgMirror=true > /usr/local/apache/cgi-bin/hg.conf.local
 fi
 
 # Sept 2017: check if genome-euro mysql server is closer
 if [ ! -f /usr/local/apache/trash/registration.txt ]; then
    # Mar 2018:  check if we can connect to genome-euro before checking what is closest
    curl -sSI genome-euro.ucsc.edu 2>&1 > /dev/null
    if [[ $? -eq 0 ]]; then
       echo comparing latency: genome.ucsc.edu Vs. genome-euro.ucsc.edu
       euroSpeed=$( (time -p (for i in `seq 10`; do curl -sSI genome-euro.ucsc.edu > /dev/null; done )) 2>&1 | grep real | cut -d' ' -f2 )
       ucscSpeed=$( (time -p (for i in `seq 10`; do curl -sSI genome.ucsc.edu > /dev/null; done )) 2>&1 | grep real | cut -d' ' -f2 )
       if [[ $(awk '{if ($1 <= $2) print 1;}' <<< "$euroSpeed $ucscSpeed") -eq 1 ]]; then
          echo genome-euro seems to be closer
          echo modifying gbib to pull data from genome-euro instead of genome
-         sed -i s/slow-db.host=genome-mysql.cse.ucsc.edu/slow-db.host=genome-euro-mysql.soe.ucsc.edu/ /usr/local/apache/cgi-bin/hg.conf
+         sed -i s/slow-db.host=genome-mysql.soe.ucsc.edu/slow-db.host=genome-euro-mysql.soe.ucsc.edu/ /usr/local/apache/cgi-bin/hg.conf
       else
          echo genome.ucsc.edu seems to be closer
          echo not modifying /usr/local/apache/cgi-bin/hg.conf
       fi
    fi
 fi
 
 touch /root/lastUpdateTime.flag
 echo - GBiB update done
 cat /etc/issue | tr -s '\n'