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
@@ -1,45 +1,49 @@
 #!/bin/bash
 source ~/.bashrc
 set -beEu -x -o pipefail
 
 #	Do not modify this script, modify the source tree copy:
 #	kent/src/hg/utils/otto/sarscov2phylo/updatePublic.sh
 
 usage() {
     echo "usage: $0 prevDate problematicSitesVcf"
 }
 
 if [ $# != 2 ]; then
   usage
   exit 1
 fi
 
 prevDate=$1
 problematicSitesVcf=$2
 
 ottoDir=/hive/data/outside/otto/sarscov2phylo
 gisaidDir=/hive/users/angie/gisaid
 
 today=$(date +%F)
 scriptDir=$(dirname "${BASH_SOURCE[0]}")
 
 $scriptDir/gisaidFromChunks.sh
 
 cogUkDir=$ottoDir/cogUk.$today
 mkdir -p $cogUkDir
 cd $cogUkDir
 $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