579d4220eec5e357b78dc0deb459db6d1858af20
chmalee
  Mon Sep 14 12:06:57 2020 -0700
Add ClinGen Gene Disease validity track to new clingen composite, refs Ana email

diff --git src/hg/utils/otto/clinGen/checkClinGen.sh src/hg/utils/otto/clinGen/checkClinGen.sh
index a2755c7..e6d32ec 100755
--- src/hg/utils/otto/clinGen/checkClinGen.sh
+++ src/hg/utils/otto/clinGen/checkClinGen.sh
@@ -1,39 +1,39 @@
 #!/bin/bash
 
 # Do not modify this script, modify the source tree copy:
 # src/hg/utils/dbVar/checkClinGen.sh
 # This script is used via a cron job and kept in $HOME/bin/scripts/
 
 set -beEu -o pipefail
 WORKDIR=$1
 
 cleanUpOnError () {
     echo "ClinGen build failed"
 } 
 
 trap cleanUpOnError ERR
 trap "cleanUpOnError;" SIGINT SIGTERM
 
 # cron jobs need to ensure this is true
 umask 002
 
 # this is where we are going to work
 if [ ! -d "${WORKDIR}" ]; then
     printf "ERROR in ClinGen build, can not find the directory: %s\n" "${WORKDIR}"
     exit 255
 fi
 
 # setup the release directory, which holds all the current bigBeds:
 mkdir -p ${WORKDIR}/release/{hg19,hg38}
 
 # There are multiple parts to this otto job, each one runs separately and does it's own
 # checking for updated files and stuff. Each downloads data from a separate website which
 # can go down so don't force the others to die just because one is having a problem.
 set +e
 ./makeCnv.sh ${WORKDIR}
 ./makeDosage.sh ${WORKDIR}
 #./makeEvRepo.sh ${WORKDIR}
-#./makeGeneValidity.sh ${WORKDIR}
+./makeGeneValidity.sh ${WORKDIR}
 set -e
 
 echo "ClinGen update done."