303adeb8a48cd1cc7a87876ab80b0620d269b227
hiram
  Tue Oct 27 12:32:10 2020 -0700
odd behavior did not recognize ~ meaning HOME refs #26428

diff --git src/hg/utils/automation/doNcbiRefSeq.pl src/hg/utils/automation/doNcbiRefSeq.pl
index 2f7db20..6a191ca 100755
--- src/hg/utils/automation/doNcbiRefSeq.pl
+++ src/hg/utils/automation/doNcbiRefSeq.pl
@@ -827,31 +827,31 @@
 
 mkdir -p $gbdbDir
 ln -f -s `pwd`/\$db.rna.fa $gbdbDir/seqNcbiRefSeq.rna.fa
 hgLoadSeq -drop -seqTbl=seqNcbiRefSeq -extFileTbl=extNcbiRefSeq \$db $gbdbDir/seqNcbiRefSeq.rna.fa
 
 hgLoadPsl \$db -table=ncbiRefSeqPsl process/\$asmId.\$db.psl.gz
 
 if [ -s process/\$asmId.rna.cds ]; then
   zcat process/\$asmId.rna.cds | grep '[0-9]\\+\\.\\.[0-9]\\+' \\
     | pslMismatchGapToBed -cdsFile=stdin -db=\$db -ignoreQNamePrefix=X \\
       process/\$asmId.\$db.psl.gz $dbTwoBit \\
         \$db.rna.fa ncbiRefSeqGenomicDiff || true
 
   rm -f $gbdbDir/ncbiRefSeqGenomicDiff.bb
   if [ -s ncbiRefSeqGenomicDiff.bed ]; then
-    bedToBigBed -type=bed9+ -tab -as=~/kent/src/hg/lib/txAliDiff.as \\
+    bedToBigBed -type=bed9+ -tab -as=\${HOME}/kent/src/hg/lib/txAliDiff.as \\
       ncbiRefSeqGenomicDiff.bed process/\$db.chrom.sizes ncbiRefSeqGenomicDiff.bb
     ln -s `pwd`/ncbiRefSeqGenomicDiff.bb $gbdbDir/ncbiRefSeqGenomicDiff.bb
   else
     rm -f ncbiRefSeqGenomicDiff.bed
   fi
 fi
 
 if [ -d "/usr/local/apache/htdocs-hgdownload/goldenPath/archive" ]; then
  gtfFile=`ls \$db.*.ncbiRefSeq.gtf.gz`
  mkdir -p /usr/local/apache/htdocs-hgdownload/goldenPath/archive/\$db/ncbiRefSeq
  rm -f /usr/local/apache/htdocs-hgdownload/goldenPath/archive/\$db/ncbiRefSeq/\$gtfFile
  ln -s `pwd`/\$db.*.ncbiRefSeq.gtf.gz \\
    /usr/local/apache/htdocs-hgdownload/goldenPath/archive/\$db/ncbiRefSeq/
 fi