85c0a7c33e839c9f6226dbcca902253df97692e5
hiram
  Fri Jun 12 11:37:40 2020 -0700
better method of getting the version of RM recommended per MarkDrefs #25720

diff --git src/hg/utils/automation/doRepeatMasker.pl src/hg/utils/automation/doRepeatMasker.pl
index fbd1b125..5699889 100755
--- src/hg/utils/automation/doRepeatMasker.pl
+++ src/hg/utils/automation/doRepeatMasker.pl
@@ -311,36 +311,36 @@
 
   $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 Open-4.0.\\
   1996-2010 <http://www.repeatmasker.org>.\\
 \\
 VERSION:\\n" > ../versionInfo.txt
 
 ./dummyRun.csh | grep -v "dev/null" >> ../versionInfo.txt
 
-grep 'version of RepeatMasker\$' $RepeatMasker >> ../versionInfo.txt
+$RepeatMasker -v >> ../versionInfo.txt
 grep RELEASE $RepeatMaskerPath/Libraries/RepeatMaskerLib.embl >> ../versionInfo.txt
 printf "# RepeatMasker engine: %s\\n" "${RepeatMaskerEngine}" >> ../versionInfo.txt
 
 ls -ld $RepeatMaskerPath $RepeatMasker
-grep 'version of RepeatMasker\$' $RepeatMasker
+$RepeatMasker -v
 grep RELEASE $RepeatMaskerPath/Libraries/RepeatMaskerLib.embl
 echo "# RepeatMasker engine: $RepeatMaskerEngine"
 _EOF_
   );
   if ($opt_useRMBlastn) {
     $bossScript->add(<<_EOF_
 printf "# using rmblastn:\\n" >> ../versionInfo.txt
 echo "# useRMBlastn: rmblastn:"
 grep RMBLAST_DIR $RepeatMaskerPath/RepeatMaskerConfig.pm | grep rmblastn-2 | awk '{print \$NF}' >> ../versionInfo.txt
 _EOF_
     );
   }
   if ($opt_useHMMER) {
     $bossScript->add(<<_EOF_
 printf "# using Dfam library and HMMER3:\\n" >> ../versionInfo.txt