7164821eac1d076015e892bc6b3961f5760f382d
chmalee
  Fri May 8 09:56:05 2020 -0700
Adding NCBI Conflict SVs track as a companion to common svs, refs #25424

diff --git src/hg/utils/otto/dbVar/checkDbVar.sh src/hg/utils/otto/dbVar/checkDbVar.sh
index 6a6f844..14109ae 100755
--- src/hg/utils/otto/dbVar/checkDbVar.sh
+++ src/hg/utils/otto/dbVar/checkDbVar.sh
@@ -1,50 +1,52 @@
 #!/bin/bash
 
 #	Do not modify this script, modify the source tree copy:
 #	src/hg/utils/dbVar/checkDbVar.sh
 #	This script is used via a cron job and kept in $HOME/bin/scripts/
 
 set -beEu -o pipefail
 WORKDIR=$1
 
 cleanUpOnError () {
     echo "dbVar build failed"
 } 
 
 trap cleanUpOnError ERR
 trap "cleanUpOnError; exit 1" SIGINT SIGTERM
 umask 002
 
 #	cron jobs need to ensure this is true
 
 #	this is where we are going to work 
 if [ ! -d "${WORKDIR}" ]; then
     printf "ERROR in dbVar build, can not find the directory: %s\n" "${WORKDIR}"
     exit 255
 fi
 
 # the release directory, where gbdb symlinks will point
 if [ ! -d release ]; then
     mkdir -p ${WORKDIR}/release/{hg19,hg38}
 fi
 
 cd "${WORKDIR}"
 
 #	see if anything is changing, if so, email notify, download, and build
 wget https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/dbvarhub/hub.txt -O tempUpdate
 if [[ ! -e lastUpdate || tempUpdate -nt lastUpdate ]]; then
     printf "New dbVar track hub:\nhttps://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/dbvarhub/\n"
     today=`date +%F`
     mkdir -p $today
     cd $today
     hubClone -download https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/dbvarhub/hub.txt
     cp dbVar/hg19/common*.bb ../release/hg19/
+    cp dbVar/hg19/conflict*.bb ../release/hg19/
     cp dbVar/hg38/common*.bb ../release/hg38/
+    cp dbVar/hg38/conflict*.bb ../release/hg38/
     cd ..
     mv tempUpdate lastUpdate
     echo "dbVar update done: `date`" 
 else
     rm tempUpdate
     echo "No update"
 fi