b505b8480a63f0726316c6ef29436af0f1d55dcc
max
  Tue Mar 31 04:23:10 2020 -0700
trying to fix speed issue with GBIC, refs #25232

diff --git src/product/installer/browserSetup.sh src/product/installer/browserSetup.sh
index ce52b73..76c55d2 100644
--- src/product/installer/browserSetup.sh
+++ src/product/installer/browserSetup.sh
@@ -1372,31 +1372,31 @@
     if [ "$DBS" == "" ] ; then
         echo2 Argument error: the '"download"' command requires at least one assembly name, like hg19 or mm10.
         exit 1
     fi
 
     echo2
     echo2 Downloading databases $DBS plus hgFixed/proteome/go from the UCSC download server
     echo2
     echo2 Determining download file size... please wait...
 
     if [ "$ONLYGENOMES" == "0" ]; then
         if [[ "$DBS" =~ hg|mm|rn3|rn4|sacCer|dm3|danRer3|ce6 ]]; then
             echo2 Downloading $DBS plus hgFixed proteome go hgFixed
             MYSQLDBS="$DBS proteome uniProt go hgFixed"
         else
-            echo2 Downloading $DBS plus GenBank tables
+            echo2 Downloading $DBS plus GenBank and RefSeq tables
             MYSQLDBS="$DBS"
             GENBANKTBLS="author cell description development gbCdnaInfo gbExtFile gbLoaded \
                          gbMiscDiff gbSeq gbWarn geneName imageClone keyword library \
                          mrnaClone organism productName refLink refSeqStatus \
                          refSeqSummary sex source tissue"
         fi
     else
         MYSQLDBS="$DBS"
     fi
 
     # rsync is doing globbing itself, so switch it off temporarily
     set -f
     # use rsync to get total size of files in directories and sum the numbers up with awk
     for db in $MYSQLDBS; do
         rsync -avn $HGDOWNLOAD::mysql/$db/ $MYSQLDIR/$db/ $RSYNCOPTS | grep ^'total size' | cut -d' ' -f4 | tr -d ', ' 
@@ -1532,31 +1532,31 @@
 
 # only download a set of minimal mysql tables, to make a genome browser that is using the mysql failover mechanism
 # faster. This should be fast enough in the US West Coast area and maybe even on the East Coast.
 function downloadMinimal
 {
     DBS=$*
     if [ "$DBS" == "" ] ; then
         echo2 Argument error: the '"minimal"' command requires at least one assembly name, like hg19 or mm10.
         exit 1
     fi
 
     echo2
     echo2 Downloading minimal tables for databases $DBS 
 
     # only these db tables are copied over by default
-    minRsyncOpt="--include=cytoBand.* --include=chromInfo.* --include=cytoBandIdeo.* --include=kgColor.* --include=knownAttrs.* --include=knownGene.* --include=knownToTag.* --include=kgXref.* --include=ensemblLift.* --include=ucscToEnsemblwgEncodeRegTfbsCells.* --include=tableList.* --include=refSeqStatus.* --include=wgEncodeRegTfbsCellsV3.* --include=extFile.* --include=trackDb.* --include=grp.* --include=ucscRetroInfo5.* --include=refLink.* --include=ucscRetroSeq5.* --include=ensemblLift.* --include=knownCanonical.* --include=gbExtFile.* --include=flyBase2004Xref --include=hgFindSpec.*"
+    minRsyncOpt="--include=cytoBand.* --include=chromInfo.* --include=cytoBandIdeo.* --include=kgColor.* --include=knownAttrs.* --include=knownGene.* --include=knownToTag.* --include=kgXref.* --include=ensemblLift.* --include=ucscToEnsemblwgEncodeRegTfbsCells.* --include=tableList.* --include=refSeqStatus.* --include=wgEncodeRegTfbsCellsV3.* --include=extFile.* --include=trackDb.* --include=grp.* --include=ucscRetroInfo5.* --include=refLink.* --include=ucscRetroSeq5.* --include=ensemblLift.* --include=knownCanonical.* --include=gbExtFile.* --include=flyBase2004Xref --include=hgFindSpec.* --include=ncbiRefSeq*"
 
     # these tables are not used for searches by default. Searches are very slow. We focus on genes.
     notSearchTables='wgEncodeGencodeBasicV19 wgEncodeGencodeCompV17 wgEncodeGencodeBasicV14 wgEncodeGencodeBasicV17 wgEncode GencodeCompV14 mgcFullMrna wgEncodeGencodeBasicV7 orfeomeMrna wgEncodeGencodePseudoGeneV14 wgEncodeGencodePseudoGeneV17 wgEncodeGencodePseudoGeneV19 wgEncodeGencodeCompV7 knownGeneOld6 geneReviews transMapAlnSplicedEst gbCdnaInfo oreganno vegaPseudoGene transMapAlnMRna ucscGenePfam qPcrPrimers transMapAlnUcscGenes transMapAlnRefSeq genscan bacEndPairs fosEndPairs'
 
     # these tracks are hidden by default
     hideTracks='intronEst cons100way cons46way ucscRetroAli5 mrna'
 
     stopMysql
 
     for db in $DBS; do
        echo2 Downloading Mysql files for mysql database $db
        $RSYNC $minRsyncOpt --exclude=* --progress -avp $RSYNCOPTS $HGDOWNLOAD::mysql/$db/ $MYSQLDIR/$db/ 
        chown -R $MYSQLUSER:$MYSQLUSER $MYSQLDIR/$db
     done