967b763f92c9dc4d3e57399de0c875029d828ef1
hiram
  Tue Dec 13 20:58:42 2022 -0800
now running the next version of RepeatMasker v4.1.4 refs #29545

diff --git src/hg/utils/automation/asmHubRepeatMasker.sh src/hg/utils/automation/asmHubRepeatMasker.sh
index ebaf002..df0a113 100755
--- src/hg/utils/automation/asmHubRepeatMasker.sh
+++ src/hg/utils/automation/asmHubRepeatMasker.sh
@@ -17,44 +17,44 @@
 export dateStamp=`date "+%FT%T %s"`
 
 export asmId=$1
 export rmOutFile=$2
 export destDir=$3
 export chrSizes=""
 
 if [ -s "$destDir/$asmId.chrom.sizes" ]; then
   chrSizes="$destDir/$asmId.chrom.sizes"
 elif [ -s "../../$asmId.chrom.sizes" ]; then
   chrSizes="../../$asmId.chrom.sizes"
 fi
 
 # assume this file name pattern
 export faAlign=`echo "${rmOutFile}" | sed -e 's/sorted.fa.out/fa.align/; s/.gz//;'`
-export RepeatMaskerPath="/hive/data/staging/data/RepeatMasker210401"
+export RepeatMaskerPath="/hive/data/staging/data/RepeatMasker221107"
 
 if [ -d "${destDir}" ]; then
   cd "${destDir}"
 
   # might already be gzipped
   if [ ! -s "${faAlign}" ]; then
      faAlign="${faAlign}.gz"
   fi
   # align file only exists when RM has been run locally, not for NCBI version
   # it is OK if it is missing, can do this anyway without it
   if [ -s "${faAlign}" ]; then
-    printf "$RepeatMaskerPath/util/rmToTrackHub.pl -out \"${rmOutFile}\" -align \"${faAlign}\"\n" 1>&2
-    $RepeatMaskerPath/util/rmToTrackHub.pl -out "${rmOutFile}" -align "${faAlign}"
+    printf "$RepeatMaskerPath/util/rmToTrackHub.pl -genome \"${asmId}\" -hubname \"${asmId}\" -out \"${rmOutFile}\" -align \"${faAlign}\"\n" 1>&2
+    $RepeatMaskerPath/util/rmToTrackHub.pl -genome "${asmId}" -hubname "${asmId}" -out "${rmOutFile}" -align "${faAlign}"
     # in place same file sort using the -o output option
     sort -k1,1 -k2,2n -o "${asmId}.fa.align.tsv" "${asmId}.fa.align.tsv" &
   else
     printf "$RepeatMaskerPath/util/rmToTrackHub.pl -out \"${rmOutFile}\"\n" 1>&2
     $RepeatMaskerPath/util/rmToTrackHub.pl -out "${rmOutFile}"
   fi
   sort -k1,1 -k2,2n -o "${asmId}.sorted.fa.join.tsv" "${asmId}.sorted.fa.join.tsv" &
   wait
   bedToBigBed -tab -as=$HOME/kent/src/hg/lib/bigRmskBed.as -type=bed9+5 \
     "${asmId}.sorted.fa.join.tsv" "${chrSizes}" \
       "${asmId}.rmsk.bb" &
   if [ -s "${asmId}.fa.align.tsv" ]; then
     bedToBigBed -tab -as=$HOME/kent/src/hg/lib/bigRmskAlignBed.as \
       -type=bed3+14 "${asmId}.fa.align.tsv" "${chrSizes}" \
         "${asmId}.rmsk.align.bb" &