0b144628d7d273d266d54ddfc2151f2d34fdbc4a
chmalee
  Wed Oct 24 09:28:29 2018 -0700
Making link to gbib shared data folders relative so when gbibs are hosted on a real server the link still works, refs #22277

diff --git src/browserbox/root/updateBrowser.sh src/browserbox/root/updateBrowser.sh
index b8fe897..1197904 100755
--- src/browserbox/root/updateBrowser.sh
+++ src/browserbox/root/updateBrowser.sh
@@ -407,31 +407,31 @@
   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,".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
+sed -i '/Track Hubs/a <li><a target="_blank" href="\/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
 cat /tmp/navbar.inc | grep -v hgNear | grep -v hgVisiGene | uniq > /usr/local/apache/htdocs/inc/globalNavBar.inc
 rm /tmp/navbar.inc
 
 # patch left side menu:
 # remove encode, neandertal, galaxy, visiGene, Downloads, cancer browser, microbial, mirrors, jobs
 for i in hgNear ENCODE Neandertal galaxy VisiGene hgdownload genome-cancer microbes mirror jobs; do
     sed -i '/<A CLASS="leftbar" .*'$i'.*$/,/<HR>$/d' /usr/local/apache/htdocs/index.html
 done
 
 # patch main pages
 sed -i 's/About the UCSC Genome Bioinformatics Site/About the UCSC Genome Browser in a Box/g' /usr/local/apache/htdocs/indexIntro.html
 perl -0777 -pi -e 's/It also.+ provides.+> project. //s' /usr/local/apache/htdocs/indexIntro.html
 perl -0777 -pi -e 's/Program-driven.+ per day.//s' /usr/local/apache/htdocs/indexInfo.html