a7d8fc835322d9017fdd5d932c22aaf2b3f5c56e
hiram
  Tue Sep 2 11:12:17 2025 -0700
updated to version 2.0.7

diff --git src/hg/utils/automation/doRepeatModeler.pl src/hg/utils/automation/doRepeatModeler.pl
index f1ee03c2ff7..1ae074fbb82 100755
--- src/hg/utils/automation/doRepeatModeler.pl
+++ src/hg/utils/automation/doRepeatModeler.pl
@@ -2,38 +2,38 @@
 
 # DO NOT EDIT the /cluster/bin/scripts copy of this file --
 # edit ~/kent/src/hg/utils/automation/doRepeatModeler.pl instead.
 
 use Getopt::Long;
 use warnings;
 use strict;
 use Carp;
 use FindBin qw($Bin);
 use lib "$Bin";
 use HgAutomate;
 use HgRemoteScript;
 use HgStepManager;
 
 # Hardcoded command path:
-my $RepeatModelerPath = "/hive/data/outside/RepeatModeler-2.0.4";
+my $RepeatModelerPath = "/hive/data/outside/RepeatModeler-2.0.7";
 my $RepeatModeler = "$RepeatModelerPath/RepeatModeler";
 my $BuildDatabase = "$RepeatModelerPath/BuildDatabase";
 # configured to consume one entire ku machine node
 my $threadCount = "-threads 32";
 my $parasolOpts = "-cpu=32 -ram=128g";
 # Option defaults
-my $bigClusterHub = 'ku';
+my $bigClusterHub = 'hgwdev';
 my $workhorse = "hgwdev";
 my $defaultWorkhorse = 'hgwdev';
 
 # Option variable names, both common and peculiar to this script:
 use vars @HgAutomate::commonOptionVars;
 use vars @HgStepManager::optionVars;
 use vars qw/
     $opt_buildDir
     $opt_unmaskedSeq
     /;
 
 # Specify the steps supported with -continue / -stop:
 my $stepper = new HgStepManager(
     [ { name => 'blastDb', func => \&doBlastDb },
       { name => 'cluster',     func => \&doCluster },
@@ -139,31 +139,31 @@
 
   my $bossScript = newBash HgRemoteScript("$runDir/blastDb.bash", $workhorse,
 				      $runDir, $whatItDoes);
 
   $bossScript->add(<<_EOF_
 export asmId="${db}"
 export unmasked2Bit="${unmaskedSeq}"
 export bDatabase="${BuildDatabase}"
 
 if [ "\${unmasked2Bit}" -nt "\${asmId}.fa" ]; then
   twoBitToFa "\${unmasked2Bit}" "\${asmId}.fa"
   touch -r "\${unmasked2Bit}" "\${asmId}.fa"
 fi
 
 if [ "\${asmId}.fa" -nt "\${asmId}.nsq" ]; then
-  time (\$bDatabase -name "\${asmId}" -engine ncbi "\${asmId}.fa") > blastDb.log 2>&1
+  time (\$bDatabase -name "\${asmId}" "\${asmId}.fa") > blastDb.log 2>&1
 fi
 
 _EOF_
     );
 
   $bossScript->execute() if (! $opt_debug);
 } # sub doBlastDb
 
 #########################################################################
 # * step: cluster [bigClusterHub]
 sub doCluster {
   my $runDir = "$buildDir";
   my $paraHub = $bigClusterHub;
 
   # First, make sure previous step has completed: