1ac6479e16d76dbfce8121b3aa493c3d9122a39a
max
  Tue Sep 5 06:37:48 2023 -0700
adding otto script for malacards to git repo and adding the missing cd command, refs #26446

diff --git src/hg/utils/otto/malacards/update.sh src/hg/utils/otto/malacards/update.sh
new file mode 100755
index 0000000..d48617e
--- /dev/null
+++ src/hg/utils/otto/malacards/update.sh
@@ -0,0 +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
+# 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