a074cd2a4d68363db2f1b6381bab63363df0bded
hiram
  Tue Dec 6 13:56:52 2022 -0800
better detection of rmblastn path with new configuration file and allow chrom.sizes to be found in current directory no redmine

diff --git src/hg/utils/automation/doRepeatMasker.pl src/hg/utils/automation/doRepeatMasker.pl
index 497a1fd..017ffa4 100755
--- src/hg/utils/automation/doRepeatMasker.pl
+++ src/hg/utils/automation/doRepeatMasker.pl
@@ -331,33 +331,33 @@
 
 ./dummyRun.csh | grep -v "dev/null" >> ../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
 $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
+printf "# using rmblastn:\\t" >> ../versionInfo.txt
 echo "# useRMBlastn: rmblastn:"
-grep RMBLAST_DIR $RepeatMaskerPath/RepeatMaskerConfig.pm | grep rmblastn-2 | awk '{print \$NF}' >> ../versionInfo.txt
+grep -w value $RepeatMaskerPath/RepeatMaskerConfig.pm | grep rmblastn | awk '{print \$NF}' >> ../versionInfo.txt
 _EOF_
     );
   }
   if ($opt_useHMMER) {
     $bossScript->add(<<_EOF_
 printf "# using Dfam library and HMMER3:\\n" >> ../versionInfo.txt
 echo "# useHMMER: Dfam library: "
 ls -ld $RepeatMaskerPath/Libraries/Dfam.hmm
 grep Release: $RepeatMaskerPath/Libraries/Dfam.hmm >> ../versionInfo.txt
 echo "# useHMMER: HMMER3: "
 grep -m 1 ^HMMER3 $RepeatMaskerPath/Libraries/Dfam.hmm >> ../versionInfo.txt
 _EOF_
     );
   }
   if (length($repeatLib) > 0) {