7592170a1f176f724492f264eff0e094cc0bc316
hiram
  Mon Nov 4 03:54:26 2024 -0800
upgrade augustus binary and correct use of mktemp refs #34685

diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl
index 829c322..2d42fa7 100755
--- src/hg/utils/automation/doAssemblyHub.pl
+++ src/hg/utils/automation/doAssemblyHub.pl
@@ -1978,34 +1978,34 @@
        return;
      }
   }
 
   &HgAutomate::mustMkdir($runDir);
 
   my $whatItDoes = "run Augustus gene prediction procedures";
   my $bossScript = newBash HgRemoteScript("$runDir/doAugustus.bash",
                     $workhorse, $runDir, $whatItDoes);
 
   $bossScript->add(<<_EOF_
 export asmId=$defaultName
 
 if [ $buildDir/\$asmId.2bit -nt \$asmId.augustus.bb ]; then
   time (~/kent/src/hg/utils/automation/doAugustus.pl -ram=6g -stop=makeGp -buildDir=`pwd` -dbHost=$dbHost \\
-    -bigClusterHub=ku -species=$augustusSpecies -workhorse=$workhorse \\
+    -bigClusterHub=$bigClusterHub -species=$augustusSpecies -workhorse=$workhorse \\
     -noDbGenePredCheck -maskedSeq=$buildDir/\$asmId.2bit \$asmId) > makeDb.log 2>&1
   time (~/kent/src/hg/utils/automation/doAugustus.pl -continue=cleanup -stop=cleanup -buildDir=`pwd` -dbHost=$dbHost \\
-    -bigClusterHub=ku -species=$augustusSpecies -workhorse=$workhorse \\
+    -bigClusterHub=$bigClusterHub -species=$augustusSpecies -workhorse=$workhorse \\
     -noDbGenePredCheck -maskedSeq=$buildDir/\$asmId.2bit \$asmId) > cleanup.log 2>&1
 else
   printf "# augustus genes step previously completed\\n" 1>&2
 fi
 _EOF_
   );
   $bossScript->execute();
 } # doAugustus
 
 #########################################################################
 # * step: xenoRefGene [bigClusterHub]
 sub doXenoRefGene {
   if ($noXenoRefSeq) {
 	&HgAutomate::verbose(1, "# -noXenoRefSeq == Xeno RefSeq gene track not created\n");
 	return;