fb4ea088b4e255ba27b04ae59e86644dabe6eda7
hiram
  Thu Oct 24 23:13:25 2024 -0700
adding NCBI link outs on NCBI RefSeq gene tracks refs #34704

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index d0f51c3..abe8b96 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -507,80 +507,83 @@
 longLabel RefSeq gene predictions from NCBI
 group genes
 visibility pack
 type bigBed
 dragAndDrop subTracks
 allButtonPair on
 dataVersion $dataVersion
 html html/%s.refSeqComposite
 priority 2
 
         track ncbiRefSeq
         parent refSeqComposite on
         color 12,12,120
         shortLabel RefSeq All
         type bigGenePred
+        urls geneName=\"https://www.ncbi.nlm.nih.gov/nuccore/\$\$?report=genbank\" geneName2=\"https://www.ncbi.nlm.nih.gov/datasets/gene/\$D/?search=\$\$\"
         labelFields name,geneName,geneName2
         defaultLabelFields geneName2
         searchIndex name
         searchTrix ixIxx/%s.ncbiRefSeq.ix
         bigDataUrl bbi/%s.ncbiRefSeq.bb
         longLabel NCBI RefSeq genes, curated and predicted sets (NM_*, XM_*, NR_*, XR_*, NP_* or YP_*)
         idXref ncbiRefSeqLink mrnaAcc name
         baseColorUseCds given
         baseColorDefault genomicCodons
         priority 1\n\n" "${asmId}" "${asmId}" "${asmId}"
 
   if [ -s ${buildDir}/trackData/ncbiRefSeq/$asmId.ncbiRefSeqCurated.bb ]; then
     rm -f $buildDir/bbi/${asmId}.ncbiRefSeqCurated.bb
     rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqCurated.ix
     rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqCurated.ixx
     ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqCurated.bb $buildDir/bbi/${asmId}.ncbiRefSeqCurated.bb
     ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqCurated.ix $buildDir/ixIxx/${asmId}.ncbiRefSeqCurated.ix
     ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqCurated.ixx $buildDir/ixIxx/${asmId}.ncbiRefSeqCurated.ixx
 
     printf "        track ncbiRefSeqCurated
         color 12,12,120
         parent refSeqComposite on
         shortLabel RefSeq Curated
         longLabel NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*)
         type bigGenePred
+        urls geneName=\"https://www.ncbi.nlm.nih.gov/nuccore/\$\$?report=genbank\" geneName2=\"https://www.ncbi.nlm.nih.gov/datasets/gene/\$D/?search=\$\$\"
         labelFields name,geneName,geneName2
         defaultLabelFields geneName2
         searchIndex name
         searchTrix ixIxx/%s.ncbiRefSeqCurated.ix
         idXref ncbiRefSeqLink mrnaAcc name
         bigDataUrl bbi/%s.ncbiRefSeqCurated.bb
         baseColorUseCds given
         baseColorDefault genomicCodons
         priority 2\n\n" "${asmId}" "${asmId}"
   fi
 
   if [ -s ${buildDir}/trackData/ncbiRefSeq/$asmId.ncbiRefSeqPredicted.bb ]; then
     rm -f $buildDir/bbi/${asmId}.ncbiRefSeqPredicted.bb
     rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqPredicted.ix
     rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqPredicted.ixx
     ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqPredicted.bb $buildDir/bbi/${asmId}.ncbiRefSeqPredicted.bb
     ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqPredicted.ix $buildDir/ixIxx/${asmId}.ncbiRefSeqPredicted.ix
     ln -s ../trackData/ncbiRefSeq/$asmId.ncbiRefSeqPredicted.ixx $buildDir/ixIxx/${asmId}.ncbiRefSeqPredicted.ixx
 
     printf "        track ncbiRefSeqPredicted
         color 12,12,120
         parent refSeqComposite on
         shortLabel RefSeq Predicted
         longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*)
         type bigGenePred
+        urls geneName=\"https://www.ncbi.nlm.nih.gov/nuccore/\$\$?report=genbank\" geneName2=\"https://www.ncbi.nlm.nih.gov/datasets/gene/\$D/?search=\$\$\"
         labelFields name,geneName,geneName2
         defaultLabelFields geneName2
         searchIndex name
         searchTrix ixIxx/%s.ncbiRefSeqPredicted.ix
         idXref ncbiRefSeqLink mrnaAcc name
         bigDataUrl bbi/%s.ncbiRefSeqPredicted.bb
         baseColorUseCds given
         baseColorDefault genomicCodons
         priority 3\n\n" "${asmId}" "${asmId}"
   fi
 
   if [ -s ${buildDir}/trackData/ncbiRefSeq/$asmId.ncbiRefSeqOther.bb ]; then
     rm -f $buildDir/bbi/${asmId}.ncbiRefSeqOther.bb
     rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqOther.ix
     rm -f $buildDir/ixIxx/${asmId}.ncbiRefSeqOther.ixx