8feb86631ca19310cb56aff6970a63e69747f86e
max
  Thu Sep 26 03:16:18 2019 -0700
fixing mastermind otto based on feedback from QA, refs #24157

diff --git src/hg/utils/otto/mastermind/buildMastermind.sh src/hg/utils/otto/mastermind/buildMastermind.sh
index d5abf53..aa31da0 100755
--- src/hg/utils/otto/mastermind/buildMastermind.sh
+++ src/hg/utils/otto/mastermind/buildMastermind.sh
@@ -2,38 +2,38 @@
 #unzip mastermind.2018.11.26.csv.zip
 #mv mastermind_cited_variants_reference-2018.11.26-csv/ 2018-11-26
 #hgsql hg19 -NB -e 'select alias, chrom from chromAlias where source = "refseq";' > chromAlias.tab
 #ln -s `pwd`/mastermind.bb /gbdb/hg19/bbi/mastermind.bb
 #python mastermindToBed.py 2018-11-26/mastermind_cited_variants_reference-2018.11.26.csv 
 #bedSort mastermind.bed mastermind.bed
 #bedToBigBed -type=bed9+ -as=mastermind.as -tab mastermind.bed //hive/data/genomes/hg19/chrom.sizes  mastermind.bb
 
 set -e -o pipefail
 cd /hive/data/outside/otto/mastermind
 date=`date --iso-8601`
 mkdir -p hg19 hg38
 mkdir -p archive/$date
 hgsql hg19 -NB -e 'select alias, chrom from chromAlias where source = "refseq";' > hg19/chromAlias.tab
 hgsql hg38 -NB -e 'select alias, chrom from chromAlias where source = "refseq";' > hg38/chromAlias.tab
-wget 'https://mastermind.genomenon.com/cvr/download?build=grch37&format=csv' -O archive/$date/hg19.zip
-wget 'https://mastermind.genomenon.com/cvr/download?build=grch38&format=csv' -O archive/$date/hg38.zip
+wget -q 'https://mastermind.genomenon.com/cvr/download?build=grch37&format=csv' -O archive/$date/hg19.zip
+wget -q 'https://mastermind.genomenon.com/cvr/download?build=grch38&format=csv' -O archive/$date/hg38.zip
 unzip -o archive/$date/hg19.zip -d archive/$date
 unzip -o archive/$date/hg38.zip -d archive/$date
 python mastermindToBed.py hg19/chromAlias.tab archive/$date/mastermind_cited_variants_reference-*-grch37.csv hg19/mastermind.bed
 python mastermindToBed.py hg38/chromAlias.tab archive/$date/mastermind_cited_variants_reference-*-grch38.csv hg38/mastermind.bed
 bedSort hg19/mastermind.bed hg19/mastermind.bed
 bedSort hg38/mastermind.bed hg38/mastermind.bed
 bedToBigBed -type=bed9+ -as=mastermind.as -tab hg19/mastermind.bed /hive/data/genomes/hg19/chrom.sizes  hg19/mastermind.new.bb
 bedToBigBed -type=bed9+ -as=mastermind.as -tab hg38/mastermind.bed /hive/data/genomes/hg38/chrom.sizes  hg38/mastermind.new.bb
 curl -s https://mastermind.genomenon.com/cvr/version | cut -d\" -f4 > mastermindRelease.new.txt
 mv mastermindRelease.new.txt mastermindRelease.txt
 mv hg19/mastermind.new.bb hg19/mastermind.bb
 mv hg38/mastermind.new.bb hg38/mastermind.bb
 
 # build archive
 REL=`cat mastermindRelease.txt`
-ARCH=/hive/data/outside/otto/archive/mastermind
-mkdir -p $ARCH/$REL/{hg19,hg38}
-cp hg19/mastermind.bb $ARCH/$REL/hg19/
-cp hg38/mastermind.bb $ARCH/$REL/hg38/
-hgsql hg19 -e 'select * from trackDb where tableName="mastermind"' > $ARCH/$REL/hg19/trackDb.tab
-hgsql hg38 -e 'select * from trackDb where tableName="mastermind"' > $ARCH/$REL/hg38/trackDb.tab
+ARCH=/hive/data/inside/archive
+mkdir -p $ARCH/{hg19,hg38}/mastermind/$REL
+cp hg19/mastermind.bb $ARCH/hg19/mastermind/$REL/
+cp hg38/mastermind.bb $ARCH/hg38/mastermind/$REL/
+hgsql hg19 -e 'select * from trackDb where tableName="mastermind"' > $ARCH/hg19/mastermind/$REL/trackDb.tab
+hgsql hg38 -e 'select * from trackDb where tableName="mastermind"' > $ARCH/hg38/mastermind/$REL/trackDb.tab