da377fdc8a33c352274795c5817d8d117e03ae10
max
  Tue Oct 4 03:30:08 2022 -0700
more panelApp fixes, partially found by QA, refs #25568

diff --git src/hg/utils/otto/panelApp/updatePanelApp src/hg/utils/otto/panelApp/updatePanelApp
index 3e12fcb..cf71149 100755
--- src/hg/utils/otto/panelApp/updatePanelApp
+++ src/hg/utils/otto/panelApp/updatePanelApp
@@ -44,30 +44,32 @@
         asFname = subTrack+".as"
 
         # -extraIndex=geneName 
         cmd = "bedToBigBed -tab -as=%s -type=bed9+26 %s /hive/data/genomes/%s/chrom.sizes %s" % (asFname, bedFname, db, bbFname)
         assert(os.system(cmd)==0)
 
         # put a copy into the archive
         archBbFname = archDir+"/%s.bb" % subTrack
         shutil.copyfile(bbFname, archBbFname)
 
 def updateGbdbSymlinks():
     " update the symlinks in /gbdb. Not really necessary but kept this code just in case. "
     for db in ["hg19", "hg38"]:
         archDir = getArchDir(db)
         for subTrack in ["genes", "tandRep", "cnv"]:
+            if subTrack=="cnv" and db=="hg19":
+                continue # no cnv on hg19
             cmd = "ln -sf `pwd`/current/%s/%s.bb /gbdb/%s/panelApp/%s.bb" % (db, subTrack, db, subTrack)
             assert(os.system(cmd)==0)
 
 def flipFiles():
     " rename the .tmp files to the final filenames "
     for db in ["hg19", "hg38"]:
         archDir = getArchDir(db)
         for subTrack in ["genes", "tandRep", "cnv"]:
             if db=="hg19" and subTrack=="cnv":
                 # no cnvs for hg19 yet
                 continue
             oldFname = "current/%s/%s.bb.tmp" % (db, subTrack)
             newFname = "current/%s/%s.bb" % (db, subTrack)
             os.replace(oldFname, newFname)