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/asmHubRepeatMasker.sh src/hg/utils/automation/asmHubRepeatMasker.sh
index 02f2c92..99081f9 100755
--- src/hg/utils/automation/asmHubRepeatMasker.sh
+++ src/hg/utils/automation/asmHubRepeatMasker.sh
@@ -7,32 +7,38 @@
 set -beEu -o pipefail
 
 # ensure sort functions properly despite kluster node environment
 export LC_COLLATE=C
 
 if [ $# -ne 3 ]; then
   printf "%s\n" "usage: asmHubRepeatMasker.sh <asmId> <pathTo/*fa.out.gz> <destinationDir/>" 1>&2
   exit 255
 fi
 
 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/$asmId.chrom.sizes"
+elif [ -s "../../$admId.chrom.sizes" ]; then
+  chrSizes="../../$asmId.chrom.sizes"
+fi
 
-export chrSizes="../../$asmId.chrom.sizes"
 # assume this file name pattern
 export faAlign=`echo "${rmOutFile}" | sed -e 's/sorted.fa.out/fa.align/; s/.gz//;'`
 export RepeatMaskerPath="/hive/data/staging/data/RepeatMasker210401"
 
 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