fd95861dbf3dd970c833b11076daa0da8738b1e8 angie Fri Mar 20 16:43:31 2020 -0700 Adding 3 tracks derived from nextstrain.org: Nextstrain {Genes, Clades, Variants}. refs #25188 diff --git src/hg/utils/otto/nextstrainNcov/doUpdate.sh src/hg/utils/otto/nextstrainNcov/doUpdate.sh new file mode 100755 index 0000000..13a973e --- /dev/null +++ src/hg/utils/otto/nextstrainNcov/doUpdate.sh @@ -0,0 +1,52 @@ +#!/bin/bash +set -xbeEu -o pipefail + +# Do not modify this script, modify the source tree copy: +# kent/src/hg/utils/nextstrainNcov/doUpdate.sh + +ottoDir=/hive/data/outside/otto/nextstrainNcov +chromSizes=/hive/data/genomes/wuhCor1/chrom.sizes +gbdbDir=/gbdb/wuhCor1/nextstrain + +cd $ottoDir + +curl -s http://data.nextstrain.org/ncov.json | gunzip -c > ncov.json +if [ ! ncov.json -nt old.ncov.json ]; then + echo "Not newer" + exit 0 +fi + +today=`date +%F` +mkdir -p $today +cp -p ncov.json $today +mv ncov.json old.ncov.json + +cd $today + +#Generate bed and VCF files +$ottoDir/nextstrain.py + +# bgzip & tabix the VCF +bgzip -f nextstrainSamples.vcf +tabix -p vcf nextstrainSamples.vcf.gz + +# bigBed-ify the gene names and "clades" +bedToBigBed -type=bed4 -tab nextstrainGene.bed $chromSizes \ + nextstrainGene.bb + +sort -k2n,2n nextstrainClade.bed > nextstrainClade.sorted.bed +bedToBigBed -as=$ottoDir/nextstrainClade.as -type=bed12+2 -tab \ + nextstrainClade.sorted.bed $chromSizes \ + nextstrainClade.bb + +# Archive +mkdir -p $ottoDir/archive/$today +cp -p `pwd`/nextstrainGene.bb `pwd`/nextstrainClade.bb `pwd`/nextstrainSamples.vcf.gz{,.tbi} \ + $ottoDir/archive/$today +cp -p `pwd`/ncov.json $ottoDir/archive/$today + +# Install +ln -sf `pwd`/nextstrainGene.bb `pwd`/nextstrainClade.bb `pwd`/nextstrainSamples.vcf.gz{,.tbi} \ + $gbdbDir/ + +echo "Updated nextstrain/ncov `date`"