acd9854d3c6537ff237c597534abd5b9afbb7a75
angie
  Thu Feb 25 10:40:45 2021 -0800
Adding cron scripts for nightly update of public tree, VCFs, metadata and protobufs for hgPhyloPlace.

diff --git src/hg/utils/otto/sarscov2phylo/updatePublic.sh src/hg/utils/otto/sarscov2phylo/updatePublic.sh
new file mode 100755
index 0000000..a8737dc
--- /dev/null
+++ src/hg/utils/otto/sarscov2phylo/updatePublic.sh
@@ -0,0 +1,44 @@
+#!/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
+$scriptDir/pangolinNcbi.sh
+
+buildDir=$ottoDir/$today
+mkdir -p $buildDir
+cd $buildDir
+$scriptDir/updatePublicTree.sh $prevDate $problematicSitesVcf >& updatePublicTree.log
+
+echo OMG success\!