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 @@ -30,23 +30,23 @@ 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 &