d13f0bd04427ad790fae74040413acded3189386
angie
  Wed Mar 3 18:45:00 2021 -0800
Call gisaidFromChunks.sh and updateIdMapping.sh to keep those up to date.  Eventually will want to update GISAID+public tree.

diff --git src/hg/utils/otto/sarscov2phylo/updatePublic.sh src/hg/utils/otto/sarscov2phylo/updatePublic.sh
index 2b0690a..19b36e1 100755
--- src/hg/utils/otto/sarscov2phylo/updatePublic.sh
+++ src/hg/utils/otto/sarscov2phylo/updatePublic.sh
@@ -1,43 +1,48 @@
 #!/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/nextcladeNcbi.sh &
 $scriptDir/pangolinNcbi.sh
 
+$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