30ebf52c1ccbd592b814c18d3a68c30624a0f85d
angie
  Wed Mar 17 11:55:37 2021 -0700
Adding new updateCombinedTree.sh after updatePublicTree.sh for GISAID+public tree.  Eventually, public tree will be derived from combined tree.

diff --git src/hg/utils/otto/sarscov2phylo/updatePublic.sh src/hg/utils/otto/sarscov2phylo/updatePublic.sh
index bd7710f..0938a1a 100755
--- src/hg/utils/otto/sarscov2phylo/updatePublic.sh
+++ src/hg/utils/otto/sarscov2phylo/updatePublic.sh
@@ -31,15 +31,19 @@
 $scriptDir/getCogUk.sh >& getCogUk.log
 
 ncbiDir=$ottoDir/ncbi.$today
 mkdir -p $ncbiDir
 cd $ncbiDir
 $scriptDir/getNcbi.sh >& getNcbi.log
 
 $scriptDir/updateIdMapping.sh $gisaidDir/{metadata_batch_$today.tsv.gz,sequences_batch_$today.fa.xz}
 
 buildDir=$ottoDir/$today
 mkdir -p $buildDir
 cd $buildDir
 $scriptDir/updatePublicTree.sh $prevDate $problematicSitesVcf >& updatePublicTree.log
 
 cat hgPhyloPlace.description.txt
+
+$scriptDir/updateCombinedTree.sh $prevDate $problematicSitesVcf >& updateCombinedTree.log
+
+cat hgPhyloPlace.plusGisaid.description.txt