531083fac3b99f775f940e7b124c88a0d41fc386
hiram
  Thu Sep 17 11:20:04 2020 -0700
recover function of local lift file when on db assembly refs #24074

diff --git src/hg/utils/automation/doNcbiRefSeq.pl src/hg/utils/automation/doNcbiRefSeq.pl
index 702fa7d..72d49aa 100755
--- src/hg/utils/automation/doNcbiRefSeq.pl
+++ src/hg/utils/automation/doNcbiRefSeq.pl
@@ -302,31 +302,34 @@
   my $downloadDir = "$buildDir/download";
   &HgAutomate::mustMkdir($runDir);
 
   my $whatItDoes = "process NCBI download files into track files.";
   # Use dbHost since genePredCheck -db=$db needs database
   my $bossScript = newBash HgRemoteScript("$runDir/doProcess.bash", $dbHost,
 				      $runDir, $whatItDoes);
 
   my $genePredCheckDb = "genePredCheck -db=\$db";
   if (! $dbExists) {
     $genePredCheckDb = "genePredCheck";
   }
   my $warnOnly = "";
   $warnOnly = "-warnAndContinue" if ($toGpWarnOnly);
 
-  my $localLiftFile = "\$downloadDir/\${asmId}To\${db}.lift";
+  my $localLiftFile = "$downloadDir/${asmId}To${db}.lift";
+  if (! -s "$localLiftFile") {
+     $localLiftFile = "../download/${asmId}To${db}.lift" if (-s "../download/${asmId}To${db}.lift");
+  }
   $localLiftFile = "" if (! -s "$localLiftFile");
   $localLiftFile = $liftFile if (-s $liftFile);
   my $pslTargetSizes = "-db=\$db";
   my $fakePslSizes = "";
   if (-s "$target2bit") {
     $pslTargetSizes = "-targetSizes=\$db.chrom.sizes";
     $fakePslSizes = "-chromSize=\$db.chrom.sizes";
   }
 
   my $dbTwoBit = "$HgAutomate::clusterData/$db/$db.2bit";
   $dbTwoBit = $target2bit if (-s "$target2bit");
 
   $bossScript->add(<<_EOF_
 # establish all variables to use here