d99de4326bbf1ad8e9461d8072622dd68597d277 angie Thu Sep 30 09:57:14 2021 -0700 Invoke updateCombinedTree.sh with new arg for explicitly setting date. diff --git src/hg/utils/otto/sarscov2phylo/updatePublic.sh src/hg/utils/otto/sarscov2phylo/updatePublic.sh index a112660..20b9ed6 100755 --- src/hg/utils/otto/sarscov2phylo/updatePublic.sh +++ src/hg/utils/otto/sarscov2phylo/updatePublic.sh @@ -1,52 +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 problematicSitesVcf" } if [ $# != 1 ]; then usage exit 1 fi 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 $buildDir prevDate=$(date -d yesterday +%F) -time $scriptDir/updateCombinedTree.sh $prevDate $problematicSitesVcf >& updateCombinedTree.log +time $scriptDir/updateCombinedTree.sh $prevDate $today $problematicSitesVcf >& updateCombinedTree.log echo "" cat hgPhyloPlace.description.txt cat hgPhyloPlace.plusGisaid.description.txt # Clean up nice xz -f new*fa &