4da885c024760ff033a7bf8a3a5ea38a3eb37852
angie
  Mon Mar 1 14:08:12 2021 -0800
Instead of running nextclade on all COG-UK sequences every night, run it only on new sequences.

diff --git src/hg/utils/otto/sarscov2phylo/updatePublic.sh src/hg/utils/otto/sarscov2phylo/updatePublic.sh
index a8737dc..2b0690a 100755
--- src/hg/utils/otto/sarscov2phylo/updatePublic.sh
+++ src/hg/utils/otto/sarscov2phylo/updatePublic.sh
@@ -1,44 +1,43 @@
 #!/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
 
 today=$(date +%F)
 scriptDir=$(dirname "${BASH_SOURCE[0]}")
 
 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
 
-$scriptDir/nextcladeCogUk.sh &
-$scriptDir/nextcladeNcbi.sh
+$scriptDir/nextcladeNcbi.sh &
 $scriptDir/pangolinNcbi.sh
 
 buildDir=$ottoDir/$today
 mkdir -p $buildDir
 cd $buildDir
 $scriptDir/updatePublicTree.sh $prevDate $problematicSitesVcf >& updatePublicTree.log
 
-echo OMG success\!
+cat hgPhyloPlace.description.txt