08860b2a6b9377fd7deece38f70c17ae73455a64
hiram
  Mon Feb 3 14:46:13 2025 -0800
should be passing along the gff3 file to download directory - get the symLinked file here refs #35027

diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl
index 2d42fa7b18e..37f711013cf 100755
--- src/hg/utils/automation/doAssemblyHub.pl
+++ src/hg/utils/automation/doAssemblyHub.pl
@@ -1828,30 +1828,31 @@
   my $dupList = "";
   if ( -s "${buildDir}/download/${asmId}.remove.dups.list" ) {
     $dupList = " | (grep -v -f \"${buildDir}/download/${asmId}.remove.dups.list\"  || true)";
   }
 
   $bossScript->add(<<_EOF_
 export asmId=$defaultName
 export gffFile=$gffFile
 
 function cleanUp() {
   rm -f \$asmId.ncbiGene.genePred.gz \$asmId.ncbiGene.genePred
   rm -f \$asmId.geneAttrs.ncbi.txt
 }
 
 if [ \$gffFile -nt \$asmId.ncbiGene.bb ]; then
+  ln -s \$gffFile ./
   (gff3ToGenePred -warnAndContinue -useName \\
     -attrsOut=\$asmId.geneAttrs.ncbi.txt \$gffFile stdout \\
       2>> \$asmId.ncbiGene.log.txt || true) | genePredFilter \\
          -chromSizes=../../\$asmId.chrom.sizes stdin stdout \\
         $dupList | gzip -c > \$asmId.ncbiGene.genePred.gz
   genePredCheck \$asmId.ncbiGene.genePred.gz
   export howMany=`genePredCheck \$asmId.ncbiGene.genePred.gz 2>&1 | grep "^checked" | awk '{print \$2}'`
   if [ "\${howMany}" -eq 0 ]; then
      printf "# ncbiGene: no gene definitions found in \$gffFile\n";
      cleanUp
      exit 0
   fi
   export ncbiGenePred="\$asmId.ncbiGene.genePred.gz"
 _EOF_
   );