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