37befdf6676de0022c60966291e21e5977dba086
chmalee
  Fri Jun 19 13:46:31 2020 -0700
Adding clingen cnv and dosage otto job to source tree now that it's been running for a while, refs #25562

diff --git src/hg/utils/otto/clinGen/checkClinGen.sh src/hg/utils/otto/clinGen/checkClinGen.sh
new file mode 100755
index 0000000..a2755c7
--- /dev/null
+++ src/hg/utils/otto/clinGen/checkClinGen.sh
@@ -0,0 +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}
+set -e
+
+echo "ClinGen update done."