7f813719b7ad2dde53149de49c2ec989b9630ea7
hiram
  Tue Sep 13 12:09:58 2022 -0700
now working through augustus step refs #29811

diff --git src/hg/utils/automation/oneAndDoneBrowser.sh src/hg/utils/automation/oneAndDoneBrowser.sh
index 52f9387..4c6755b 100755
--- src/hg/utils/automation/oneAndDoneBrowser.sh
+++ src/hg/utils/automation/oneAndDoneBrowser.sh
@@ -114,34 +114,40 @@
 esac
 
 printf "# ==== %s ====\n" "`date '+%F %T %s'`" 1>&2
 printf "# working in %s\n" "${buildDir}" 1>&2
 printf "# building %s - %s\n" "${organism}" "${sciName}" 1>&2
 printf "# dbName: %s\n" "${dbName}" 1>&2
 printf "# ucscNames: %s\n" "${ucscNames}" 1>&2
 printf "# rmskSpecies: %s\n" "${rmskSpecies}" 1>&2
 printf "# augustusSpecies: %s\n" "${augustusSpecies}" 1>&2
 printf "# ncbiRmsk: %s\n" "${ncbiRmsk}" 1>&2
 if [ "x${noRmsk}y" != "xy" ]; then
   printf "# noRmsk: '%s'\n" "${noRmsk}" 1>&2
 fi
 printf "\n" 1>&2
 
+# possible steps in order:
+
+# download sequence assemblyGap chromAlias gatewayPage cytoBand gc5Base
+# repeatMasker simpleRepeat allGaps idKeys windowMasker addMask gapOverlap
+# tandemDups cpgIslands ncbiGene ncbiRefSeq xenoRefGene augustus trackDb cleanup
+
 ## export stepStart="download"
 ## export stepEnd="sequence"
-export stepStart="chromAlias"
-export stepEnd="chromAlias"
+export stepStart="ncbiGene"
+export stepEnd="augustus"
 
 printf "cd \"${buildDir}\"\n" 1>&2
 cd "${buildDir}"
 
 printf "\$HOME/kent/src/hg/utils/automation/doAssemblyHub.pl \\
   -continue=\"${stepStart}\" -stop=\"${stepEnd}\" -dbName=\"${dbName}\" \\
      -rmskSpecies=\"${rmskSpecies}\" -bigClusterHub=ku -buildDir=\`pwd\` \\
         -fileServer=hgwdev -smallClusterHub=hgwdev \\
            ${noRmsk} ${ncbiRmsk} ${ucscNames} ${augustusSpecies} \\
               -workhorse=hgwdev \"${asmId}\" >> build.log 2>&1\n" 1>&2
 
 $HOME/kent/src/hg/utils/automation/doAssemblyHub.pl \
   -continue="${stepStart}" -stop="${stepEnd}" -dbName="${dbName}" \
      -rmskSpecies="${rmskSpecies}" -bigClusterHub=ku -buildDir=`pwd` \
         -fileServer=hgwdev -smallClusterHub=hgwdev \
@@ -171,15 +177,18 @@
      defaultPos, active, orderKey, genome, scientificName,
      htmlPath, hgNearOk, hgPbOk, sourceName, taxId)
 VALUES\n" >> dbDbInsert.sql
 printf "(\"%s\", \"%s (%s/%s)\", \"/gbdb/%s\", \"%s\",
    \"%s\", 1, %d, \"%s\", \"%s\", \"/gbdb/%s/html/description.html\", 0,
      1, \"%s\", %d);\n" "${dbName}" "${asmDate}" "${asmName}" "${dbName}" "${dbName}" "${comName}" "${defaultPos}" "${orderKey}" "${comName}" "${sciName}" "${dbName}" "${accessionID}" "${taxId}" >> dbDbInsert.sql
 
 fi
 
 printf "# dbDbInsert.sql statement is completed:\n" 1>&2
 cat dbDbInsert.sql 1>&2
 
 if [ ! -s "chrom.sizes" ]; then
   ln -s $dbName.chrom.sizes chrom.sizes
 fi
+if [ ! -d "bed" ]; then
+  ln -s trackData bed
+fi