e3c90a0c1514cc8f4e0bf17618fd2d2d06e235ef
hiram
  Mon May 2 10:16:21 2022 -0700
clean up loose ends no redmine

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index 4ba5d52..b246373 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -335,30 +335,36 @@
 
 ### assume there is no ncbiRefSeq track
 ### when there is, this will eliminate the ncbiGene track
 ### and it figures into setting the visibility of the augustus gene track
 export haveNcbiRefSeq="no"
 
 ###################################################################
 # ncbiRefSeq composite track
 if [ -s ${buildDir}/trackData/ncbiRefSeq/$asmId.ncbiRefSeq.bb ]; then
 rm -f $buildDir/bbi/${asmId}.ncbiRefSeq.bb
 rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeq.ix
 rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeq.ixx
 ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeq.bb $buildDir/bbi/${asmId}.ncbiRefSeq.bb
 ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeq.ix $buildDir/ixIxx/${asmId}.ncbiRefSeq.ix
 ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeq.ixx $buildDir/ixIxx/${asmId}.ncbiRefSeq.ixx
+if [ -s ${buildDir}/trackData/ncbiRefSeq/${asmId}*.ncbiRefSeq.gtf.gz ]; then
+    mkdir -p $buildDir/genes
+    rm -f ${buildDir}/genes/${asmId}.ncbiRefSeq.gtf.gz
+    gtfFile=`ls ${buildDir}/trackData/ncbiRefSeq/${asmId}*.ncbiRefSeq.gtf.gz|tail -1|sed -e 's#.*/##;'`
+    ln -s ../trackData/ncbiRefSeq/${gtfFile} ${buildDir}/genes/${asmId}.ncbiRefSeq.gtf.gz
+fi
 
   export dataVersion="html/ncbiRefSeqVersion.txt"
   if [ -s ${buildDir}/trackData/ncbiRefSeq/$asmId.ncbiRefSeqVersion.txt ]; then
    dataVersion=`cat ${buildDir}/trackData/ncbiRefSeq/$asmId.ncbiRefSeqVersion.txt`
   fi
 
   printf "track refSeqComposite
 compositeTrack on
 shortLabel NCBI RefSeq
 longLabel RefSeq gene predictions from NCBI
 group genes
 visibility pack
 type bigBed
 dragAndDrop subTracks
 allButtonPair on