d98fc157940421537cb42251aee01a245c88c943
max
  Wed Apr 1 08:45:49 2020 -0700
adding encRegTfbsClusteredSources to GBIC download script, refs #25232

diff --git src/product/installer/browserSetup.sh src/product/installer/browserSetup.sh
index 76c55d2..1859b8a 100644
--- src/product/installer/browserSetup.sh
+++ src/product/installer/browserSetup.sh
@@ -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.* --include=ncbiRefSeq*"
+    minRsyncOpt="--include=cytoBand.* --include=chromInfo.* --include=cytoBandIdeo.* --include=kgColor.* --include=knownAttrs.* --include=knownGene.* --include=knownToTag.* --include=kgXref.* --include=ensemblLift.* --include=ucscToEnsembl.* --include=wgEncodeRegTfbsCells.* --include=encRegTfbsClusteredSources.* --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