e1b3625f3a40bfee5c483284fa7f6b23bf6bd47d
max
  Tue Aug 21 13:18:40 2018 +0200
moving all config files in GBIB to the new .gi.ucsc.edu domain names
from the old .soe.ucsc.edu domain names. refs #21876
This commit only changes the versions of these files in the repo,
not the ones in the actual browserbox, as they still need to get
pushed into the browserbox, either by the pusing procedure from
hgdownload or by the build meister when he builds the GBIB VM image.
See
http://genomewiki.ucsc.edu/genecats/index.php/Gbib_release#Release_config_changes_to_GbIb
and the related pages in the genecats genomewiki.

diff --git src/browserbox/root/updateBrowser.sh src/browserbox/root/updateBrowser.sh
index b8fe897..131cda2 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.soe.ucsc.edu"
+RSYNCSRC="rsync://hgdownload.gi.ucsc.edu"
 RSYNCCGIBIN=cgi-bin
 RSYNCHTDOCS=htdocs
-UPDATEFLAG=http://hgdownload.soe.ucsc.edu/gbib/lastUpdate
+UPDATEFLAG=http://hgdownload.gi.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 
@@ -98,59 +98,59 @@
 if [ "$#" -eq 0 ] ; then
     if modprobe vboxguest 2> /dev/null > /dev/null; then
        if VBoxControl guestproperty get gbibAutoUpdateOff | grep -xq "Value: yes" 2> /dev/null ; then
            exit 6
        fi
     fi
 # show a little note when VirtualBox kernel module is not working and we're not running under cron
 else
     if [ ! modprobe vboxguest 2> /dev/null > /dev/null ] ; then
       echo - Info: GBiB not running on VirtualBox or VirtualBox Guest Utils are not working
     fi
 fi
 
 
 # check if we have internet, stop if not
-wget -q --tries=1 --timeout=10 --spider http://hgdownload.soe.ucsc.edu -O /dev/null
+wget -q --tries=1 --timeout=10 --spider http://hgdownload.gi.ucsc.edu -O /dev/null
 if [ $? -ne 0 ] ; then
-    echoDebug GBiB has no connection to hgdownload.soe.ucsc.edu, cannot update now
+    echoDebug GBiB has no connection to hgdownload.gi.ucsc.edu, cannot update now
     exit 3
 fi
 
 # check flag file if run with no parameter (=from cron)
 if [ "$#" -eq 0 ] ; then
    # check a flag file to see if anything on hgdownload actually changed
    if /root/urlIsNotNewerThanFile $UPDATEFLAG /root/lastUpdateTime.flag
    then
        exit 0
    fi
 fi
 
 # unless already calling self, update self and call self unless doing only cgis
 # self-updates are not done when suppressed with notSelf and also not in hgwdev-mode to allow testing of local updateBrowser.sh changes
 # Internal sidenote: if you want hgwdev CGIs and also the current hgwdev update
 # script, do a gbibCoreUpdateBeta+updateBrowser hgwdev
 
 # gbibCoreUpdateBeta ends with -Beta because it is used during beta time, to
 # test the current dev update script The update script itself has only a
 # two-stage release process, beta and final, as the alpha version of the script
 # is on the GBiB of the developer itself.
 # the file /root/gbibSkipUpdate allows to skip one single auto-update
 if [[ ( "$BASH_ARGV" != "notSelf" && "$1" != "hgwdev" ) && ( ! -e /root/gbibSkipNextUpdate ) ]] ; then
     echo getting new update script
     # we got three VMs where updateBrowser.sh was 0 bytes, so doing download/move now
-    wget http://hgdownload.soe.ucsc.edu/gbib/updateBrowser.sh -O /root/updateBrowser.sh.new -q && mv /root/updateBrowser.sh.new /root/updateBrowser.sh
+    wget http://hgdownload.gi.ucsc.edu/gbib/updateBrowser.sh -O /root/updateBrowser.sh.new -q && mv /root/updateBrowser.sh.new /root/updateBrowser.sh
     chmod a+x /root/updateBrowser.sh
     /root/updateBrowser.sh $1 notSelf
     exit 0
 fi
 
 rm -f /root/gbibSkipNextUpdate
 
 # check if any hgMirror jobs are running right now
 # check if the group id file exists and also if any processes exist with this group id
 # note that the .pid actually contains a group id, not a process id
 if [ -f /tmp/lastJob.pid ] && [ "$(ps x -o pgid | grep $(cat /tmp/lastJob.pid) | wc -l)" != "0" ] ; then
     echo a hgMirror job is running right now, not updating
     exit 4
 fi
 	
@@ -286,47 +286,47 @@
     	htmlExt="-"$dirExt
     fi
 
     RSYNCAPACHE="$RSYNCOPTS --delete"
 
      # remove a lot of clutter that accumulated in hgwdev's alpha cgi-bin dir
     if [ "$dirExt" == "alpha" ] ; then
       RSYNCAPACHE="$RSYNCAPACHE --exclude ENCODE/**.pdf --exclude *.gz --exclude *.bw --exclude *.bb --exclude *.bam --exclude goldenPath/**.pdf --exclude admin/** --exclude goldenPath/customTracks/** --exclude pubs/** --exclude ancestors/** --exclude training/** --exclude trash --exclude style-public/** --exclude js-public/** --exclude **/edw* --exclude images/mammalPsg/** --exclude **/encodeTestHub* --exclude favicon.ico --exclude folders --exclude ENCODE/** --exclude ENCODE/** --exclude Neandertal/** --exclude gbib/** --exclude generator/** --exclude js-*/** --exclude js/*/* --exclude .\* --exclude x86_64/* --exclude .xauth --exclude .hg.conf --exclude hgHeatmap* --exclude hg.conf --exclude 'hgt/**' --exclude admin/** --exclude images --exclude trash --exclude edw* --exclude visiGeneData/** --exclude crom_dir/ --exclude testp/ --exclude *.exe --exclude *.old --exclude *.tmp --exclude *.bak --exclude test* --exclude hg.conf* --exclude **/hgHeatmap* --exclude ~* --exclude Intronerator** --exclude hgText --exclude hgSubj --exclude gisaid* --exclude nt4.dir --exclude qaPush* --exclude docIdView --exclude ct/ --exclude *.bak --exclude hg.conf* --exclude gsid*/ --exclude *.private --exclude useCount --exclude ~* --exclude lssnp/ --exclude hg.conf.local"
     fi
   
     # remove things that are on hgwdev beta directories but not necessary on the gbib
     if [ "$dirExt" == "beta" ] ; then
       RSYNCAPACHE="$RSYNCAPACHE --exclude favicon*.ico --exclude hg.conf* --exclude ENCODE --exclude *.gz --exclude *.bw --exclude *.bb --exclude *.bam --exclude goldenPath/**.pdf --exclude admin --exclude goldenPath/customTracks --exclude pubs --exclude ancestors --exclude training --exclude trash --exclude .htaccess --exclude htdocs --exclude Neandertal --exclude RNA-img --exclude ebola --exclude encodeDCC --exclude evoFold --exclude geneExtra --exclude js-public --exclude style-public --exclude hgNearData --exclude visiGeneData --exclude visiGene"
     fi
 
-    rsync $RSYNCAPACHE $user@hgwdev.soe.ucsc.edu:/usr/local/apache/htdocs${htmlExt}/ /usr/local/apache/htdocs/
-    rsync $RSYNCAPACHE $user@hgwdev.soe.ucsc.edu:/usr/local/apache/cgi-bin${cgiExt}/ /usr/local/apache/cgi-bin/
+    rsync $RSYNCAPACHE $user@hgwdev.gi.ucsc.edu:/usr/local/apache/htdocs${htmlExt}/ /usr/local/apache/htdocs/
+    rsync $RSYNCAPACHE $user@hgwdev.gi.ucsc.edu:/usr/local/apache/cgi-bin${cgiExt}/ /usr/local/apache/cgi-bin/
 
-    PUSHLOC=$user@hgwdev.soe.ucsc.edu:/usr/local/apache/htdocs/gbib/push/
+    PUSHLOC=$user@hgwdev.gi.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.soe.ucsc.edu::gbib/push/
+    PUSHLOC=hgdownload.gi.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.soe.ucsc.edu/gbdb/ /data/gbdb/
+  rsync $RSYNCOPTS --existing rsync://hgdownload.gi.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.soe.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.gi.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.soe.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.gi.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,".soe.ucsc.edu") WHERE host not like "%ucsc.edu"'
+  mysql hgcentral -e 'UPDATE blatServers SET host=CONCAT(host,".gi.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.soe.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.gi.ucsc.edu/slow-db.host=genome-euro-mysql.gi.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'