e0eafd3f09d381d9f2ccd04beada00f54c44b115 max Thu Jun 20 04:18:03 2024 -0700 make otto job quiet, no redmine diff --git src/hg/utils/otto/malacards/update.sh src/hg/utils/otto/malacards/update.sh index d48617e..8abcada 100755 --- src/hg/utils/otto/malacards/update.sh +++ src/hg/utils/otto/malacards/update.sh @@ -1,20 +1,20 @@ #!/bin/bash # redmine 14417 set -e -o pipefail now=`date -I` cd /hive/data/outside/otto/malacards -wget https://genecardscustomers.blob.core.windows.net/ucsc/UCSC_DiseaseCentric_dump_MC_current.csv -O oldVersions/$now.csv +wget -q https://genecardscustomers.blob.core.windows.net/ucsc/UCSC_DiseaseCentric_dump_MC_current.csv -O oldVersions/$now.csv # copied from ~/kent/src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes16.sh # load malacards table hgsql hg38 -e 'drop table malacards; create table malacards (geneSymbol varchar(255), maladySymbol varchar(255), urlSuffix varchar(255), mainName varchar(255), geneScore float, diseaseScore float, isElite bool)' hgsql hg38 -e 'create index malacardsGeneIdx on malacards(geneSymbol);' s='"'; hgsql hg38 -e "delete from malacards; load data local infile ${s}oldVersions/$now.csv${s} into table malacards columns terminated by ',' enclosed by '$s' escaped by '' ignore 1 lines" # load knownToMalacards tables kent=~/kent for db in hg38 hg19; do hgsql -e "select geneSymbol,kgId from kgXref" --skip-column-names $db | awk '{if (NF == 2) print}' | sort > geneSymbolToKgId.txt hgsql -e "select geneSymbol from malacards" --skip-column-names $db | sort > malacardExists.txt join malacardExists.txt geneSymbolToKgId.txt | awk 'BEGIN {OFS="\t"} {print $2, $1}' > knownToMalacard.txt hgLoadSqlTab -notOnServer $db knownToMalacards $kent/src/hg/lib/knownTo.sql knownToMalacard.txt done echo Malacards update OK