07239334f514fc80e68aba6968335e56853e3177
hiram
  Tue Sep 2 11:23:25 2025 -0700
upgrade to version 4.2.1

diff --git src/hg/utils/automation/doRepeatMasker.pl src/hg/utils/automation/doRepeatMasker.pl
index b00d903e403..17dd0f2663b 100755
--- src/hg/utils/automation/doRepeatMasker.pl
+++ src/hg/utils/automation/doRepeatMasker.pl
@@ -4,31 +4,31 @@
 # edit ~/kent/src/hg/utils/automation/doRepeatMasker.pl instead.
 
 # $Id: doRepeatMasker.pl,v 1.14 2009/03/19 16:15:29 hiram Exp $
 
 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 $RepeatMaskerPath = "/hive/data/outside/RepeatMasker/RepeatMasker-4.1.7-p1";
+my $RepeatMaskerPath = "/hive/data/outside/RepeatMasker/RepeatMasker-4.2.1";
 my $RepeatMasker = "$RepeatMaskerPath/RepeatMasker";
 # default engine changed from crossmatch to rmblast as of 2022-12
 # with RM version 4.1.4
 my $RepeatMaskerEngine = "-engine rmblast -pa 1";
 # per RM doc, rmblast uses 4 CPUs for each job
 my $parasolRAM = "-cpu=4 -ram=32g";
 
 # Option variable names, both common and peculiar to this script:
 use vars @HgAutomate::commonOptionVars;
 use vars @HgStepManager::optionVars;
 use vars qw/
     $opt_buildDir
     $opt_ncbiRmsk
     $opt_dupList
     $opt_liftSpec
@@ -324,32 +324,32 @@
 
   my $whatItDoes =
 "It computes a logical partition of unmasked 2bit into 500k chunks
 and runs it on the cluster with the most available bandwidth.";
   my $bossScript = new HgRemoteScript("$runDir/doCluster.csh", $paraHub,
 				      $runDir, $whatItDoes);
 
   $bossScript->add(<<_EOF_
 
 chmod a+x dummyRun.csh
 chmod a+x RMRun.csh
 
 # Record RM version used:
 printf "The repeat files provided for this assembly were generated using RepeatMasker.\\
   Smit, AFA, Hubley, R & Green, P.,\\
-  RepeatMasker version 4.1.4\\
-  1996-2010 <http://www.repeatmasker.org>.\\
+  RepeatMasker version 4.2.1\\
+  1996-2025 <http://www.repeatmasker.org>.\\
 \\
 VERSION:\\n" > ../versionInfo.txt
 
 ./dummyRun.csh | grep -v "dev/null" >> ../versionInfo.txt
 
 $RepeatMasker -v >> ../versionInfo.txt
 printf "# RMRBMeta.embl library version: %s\\n" "`grep RELEASE $RepeatMaskerPath/Libraries/RMRBMeta.embl`" >> ../versionInfo.txt
 printf "# RepeatMasker engine: %s\\n" "${RepeatMaskerEngine}" >> ../versionInfo.txt
 
 ls -ld $RepeatMaskerPath $RepeatMasker
 $RepeatMasker -v
 echo -n "# RMRBMeta.embl library version: "
 grep RELEASE $RepeatMaskerPath/Libraries/RMRBMeta.embl | sed -e 's/  *\\*\$//;'
 echo "# RepeatMasker engine: $RepeatMaskerEngine"
 _EOF_