67eb161b05397c50dcfb3c7ec1b60654b15d66d2
hiram
  Mon Sep 15 13:00:04 2025 -0700
fixed rmToTrackHub.pl script from Robert

diff --git src/hg/utils/automation/doRepeatMasker.pl src/hg/utils/automation/doRepeatMasker.pl
index edb711a7480..78d5559a788 100755
--- src/hg/utils/automation/doRepeatMasker.pl
+++ src/hg/utils/automation/doRepeatMasker.pl
@@ -620,31 +620,31 @@
   my $bossScript = newBash HgRemoteScript("$runDir/doLoad.bash", $dbHost,
 				      $runDir, $whatItDoes);
 
   $split = "-nosplit";
   $split = "-split" if ($opt_splitTables);
   my $installDir = "$HgAutomate::clusterData/$db";
   $bossScript->add(<<_EOF_
 export db=$db
 
 # ensure sort functions properly despite kluster node environment
 export LC_COLLATE=C
 
 hgLoadOut -table=rmsk$updateTable $split \$db \$db.sorted.fa.out
 hgLoadOut -verbose=2 -tabFile=\$db.rmsk$updateTable.tab -table=rmsk$updateTable -nosplit \$db \$db.sorted.fa.out 2> \$db.bad.records.txt
 # construct bbi files for assembly hub
-$RepeatMaskerPath/util/rmToTrackHub.pl -out \$db.sorted.fa.out -align \$db.fa.align
+$RepeatMaskerPath/util/rmToTrackHub.pl -chromsizes=../../chrom.sizes -out \$db.sorted.fa.out -align \$db.fa.align
 # in place same file sort using the -o output option
 awk -F\$'\\t' '\$15 > -1 && \$13 > -1' \$db.fa.align.tsv | sort -k1,1 -k2,2n > t.tsv
 rm -f \$db.fa.align.tsv
 mv t.tsv \$db.fa.align.tsv
 # sort -k1,1 -k2,2n -o \$db.fa.align.tsv \$db.fa.align.tsv &
 sort -k1,1 -k2,2n -o \$db.sorted.fa.join.tsv \$db.sorted.fa.join.tsv
 wait
 bedToBigBed -tab -as=\$HOME/kent/src/hg/lib/bigRmskAlignBed.as -type=bed3+14 \\
   \$db.fa.align.tsv ../../chrom.sizes \$db.rmsk.align.bb &
 bedToBigBed -tab -as=\$HOME/kent/src/hg/lib/bigRmskBed.as -type=bed9+5 \\
   \$db.sorted.fa.join.tsv ../../chrom.sizes \$db.rmsk.bb
 wait
 rm -fr classBed classBbi rmskClass
 mkdir classBed classBbi rmskClass
 sort -k12,12 \$db.rmsk$updateTable.tab \\