fe1290a83aa62636e7f26092751571e016818493
hiram
  Thu Jan 5 16:59:10 2023 -0800
correct NCBI Nucleotide database outlink and now with gap track no redmine

diff --git src/hg/utils/automation/faToHub.sh src/hg/utils/automation/faToHub.sh
index 15513e4..d988445 100755
--- src/hg/utils/automation/faToHub.sh
+++ src/hg/utils/automation/faToHub.sh
@@ -110,31 +110,31 @@
         | sort -k1,1 -k2,2n > $asmId.assembly.bed
   zgrep -v "^#" ../../$asmId.agp.gz | awk '$5 == "N" || $5 == "U"' \
      | awk '{printf "%s\t%d\t%d\t%s\n", $1, $2-1, $3, $8}' \
         | sort -k1,1 -k2,2n > $asmId.gap.bed
 
   bedToBigBed -extraIndex=name -verbose=0 $asmId.assembly.bed \
     ../../$asmId.chrom.sizes.txt $asmId.assembly.bb
   touch -r ../../$asmId.agp.gz $asmId.assembly.bb
   $HOME/kent/src/hg/utils/automation/genbank/nameToIx.pl \
     $asmId.assembly.bed | sort -u > $asmId.assembly.ix.txt
   if [ -s $asmId.assembly.ix.txt ]; then
     ixIxx $asmId.assembly.ix.txt $asmId.assembly.ix $asmId.assembly.ixx
   fi
   if [ -s "${asmId}.gap.bed" ]; then
     bedToBigBed -extraIndex=name -verbose=0 $asmId.gap.bed \
-      ../../$asmId.chrom.sizes $asmId.gap.bb
+      ../../$asmId.chrom.sizes.txt $asmId.gap.bb
     touch -r ../../$asmId.agp.gz $asmId.gap.bb
     rm -f ${destDir}/bbi/$asmId.gap.bb
     ln -s ../trackData/assemblyGap/$asmId.gap.bb ${destDir}/bbi/$asmId.gap.bb
   else
     rm -f "${asmId}.gap.bed"
   fi
 else
   printf "# assembly/gap previously completed\n" 1>&2
 fi
 
 cd "${destDir}"
 
 if [ -s "${destDir}/trackData/assemblyGap/$asmId.assembly.bb" ]; then
   rm -f ${destDir}/bbi/$asmId.assembly.bb
   ln -s ../trackData/assemblyGap/$asmId.assembly.bb ${destDir}/bbi/$asmId.assembly.bb
@@ -145,42 +145,65 @@
   fi
 
   printf "
 track assembly
 longLabel Assembly
 shortLabel Assembly
 visibility pack
 colorByStrand 150,100,30 230,170,40
 color 150,100,30
 altColor 230,170,40
 bigDataUrl bbi/$asmId.assembly.bb
 type bigBed 6
 html html/$asmId.assembly
 searchIndex name
 searchTrix ixIxx/$asmId.assembly.ix
-url https://www.ncbi.nlm.nih.gov/nuccore/$$
+url https://www.ncbi.nlm.nih.gov/nuccore/\$\$
 urlLabel NCBI Nucleotide database
 group map
 " >> ${destDir}/hub.txt
 
 printf "<h1>assembly track description page</h1>
 <p>
 Should be filled in with information about this track.
 </p>\n" > ${destDir}/html/$asmId.assembly.html
 
 fi
 
+if [ -s "${destDir}/trackData/assemblyGap/$asmId.gap.bb" ]; then
+  rm -f ${destDir}/bbi/$asmId.gap.bb
+  ln -s ../trackData/assemblyGap/$asmId.gap.bb ${destDir}/bbi/$asmId.gap.bb
+
+  printf "
+track gap
+longLabel AGP gap
+shortLabel Gap (AGP defined)
+visibility dense
+color 0,0,0
+bigDataUrl bbi/$asmId.gap.bb
+type bigBed 4
+group map
+html html/$asmId.gap
+" >> ${destDir}/hub.txt
+
+printf "<h1>gap track description page</h1>
+<p>
+Should be filled in with information about this track.
+</p>\n" > ${destDir}/html/$asmId.gap.html
+
+fi
+
 cd "${destDir}"
 
 ###### cytoBand ####################
 mkdir -p "${destDir}/trackData/cytoBand"
 cd "${destDir}/trackData/cytoBand"
 if [ ../../$asmId.chrom.sizes.txt -nt $asmId.cytoBand.bb ]; then
   printf "# construction cytoBand track\n" 1>&2
   awk '{printf "%s\t0\t%d\t\tgneg\n", $1, $2}' ../../$asmId.chrom.sizes.txt | sort -k1,1 -k2,2n > $asmId.cytoBand.bed
   bedToBigBed -type=bed4+1 -as=$HOME/kent/src/hg/lib/cytoBand.as -tab $asmId.cytoBand.bed ../../$asmId.chrom.sizes.txt $asmId.cytoBand.bb >> $buildLog 2>&1
 
   touch -r ../../$asmId.chrom.sizes.txt $asmId.cytoBand.bb
 else
   printf "# cytoBand previously completed\n" 1>&2
 fi