01388e26d682bc9c0f3b2cf27ae25ff989568e21
angie
  Mon May 24 10:01:27 2021 -0700
Set prevDate in this script instead of requiring it from caller.

diff --git src/hg/utils/otto/sarscov2phylo/updatePublic.sh src/hg/utils/otto/sarscov2phylo/updatePublic.sh
index dbb1e5c..a112660 100755
--- src/hg/utils/otto/sarscov2phylo/updatePublic.sh
+++ src/hg/utils/otto/sarscov2phylo/updatePublic.sh
@@ -1,53 +1,52 @@
 #!/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"
+    echo "usage: $0 problematicSitesVcf"
 }
 
-if [ $# != 2 ]; then
+if [ $# != 1 ]; then
   usage
   exit 1
 fi
 
-prevDate=$1
-problematicSitesVcf=$2
+problematicSitesVcf=$1
 
 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
 time $scriptDir/getCogUk.sh >& getCogUk.log
 
 ncbiDir=$ottoDir/ncbi.$today
 mkdir -p $ncbiDir
 cd $ncbiDir
 time $scriptDir/getNcbi.sh >& getNcbi.log
 
 time $scriptDir/updateIdMapping.sh \
     $gisaidDir/{metadata_batch_$today.tsv.gz,sequences_batch_$today.fa.xz}
 
 buildDir=$ottoDir/$today
 mkdir -p $buildDir
 cd $buildDir
-time $scriptDir/updatePublicTree.sh $prevDate $problematicSitesVcf >& updatePublicTree.log
-
-cat hgPhyloPlace.description.txt
 
+prevDate=$(date -d yesterday +%F)
 time $scriptDir/updateCombinedTree.sh $prevDate $problematicSitesVcf >& updateCombinedTree.log
 
+echo ""
+cat hgPhyloPlace.description.txt
 cat hgPhyloPlace.plusGisaid.description.txt
 
 # Clean up
 nice xz -f new*fa &