f9ce722d011fb87c9f61a4d892b9140ef7fa9047
hiram
  Mon Sep 12 20:38:56 2022 -0700
now working through step chromAlias and fixup that procedure to work correctly on ucsc names refs #29811

diff --git src/hg/utils/automation/oneAndDoneBrowser.sh src/hg/utils/automation/oneAndDoneBrowser.sh
index 935459e..52f9387 100755
--- src/hg/utils/automation/oneAndDoneBrowser.sh
+++ src/hg/utils/automation/oneAndDoneBrowser.sh
@@ -114,62 +114,72 @@
 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
 
-export stepStart="download"
-export stepEnd="sequence"
+## export stepStart="download"
+## export stepEnd="sequence"
+export stepStart="chromAlias"
+export stepEnd="chromAlias"
 
 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 \
            ${noRmsk} ${ncbiRmsk} ${ucscNames} ${augustusSpecies} \
               -workhorse=hgwdev "${asmId}" >> build.log 2>&1
 
 cd "${buildDir}"
+
+if [ "download/${asmId}_assembly_report.txt" -nt "${dbName}.config.ra" ]; then
+
 $HOME/kent/src/hg/utils/automation/prepConfig.pl "${dbName}" \
   "${hgCentralClade}" "${trackDbDir}" download/${asmId}_assembly_report.txt \
        > ${dbName}.config.ra
 
 export taxId=`grep "^taxId" ${dbName}.config.ra | awk '{print $NF}'`
 export asmDate=`grep "^assemblyDate" ${dbName}.config.ra | sed -e "s/assemblyDate \+//"`
 export asmName=`grep "^ncbiAssemblyName" ${dbName}.config.ra | sed -e "s/ncbiAssemblyName \+//"`
 export comName=`grep "^commonName" ${dbName}.config.ra | sed -e "s/commonName \+//"`
 export sciName=`grep "^scientificName" ${dbName}.config.ra | sed -e "s/scientificName \+//"`
 export orderKey=`grep "^orderKey" ${dbName}.config.ra | sed -e "s/orderKey \+//"`
 export accessionID=`grep "^genBankAccessionID" ${dbName}.config.ra | sed -e "s/genBankAccessionID \+//"`
 export defaultPos=`head -1 $dbName.chrom.sizes | awk '{end=int($2/2)+9999; if (end > $2){end = $2}; printf "%s:%d-%d", $1, int($2/2), end}'`
 
-printf "where is the invalid number\n"
-echo "${dbName}" "${asmDate}" "${asmName}" "${dbName}" "${dbName}" "${comName}" "${defaultPos}" "${orderKey}" "${comName}" "${sciName}" "${dbName}" "${accessionID}"
-
 printf "DELETE from dbDb where name = \"%s\";\n" "${dbName}" > dbDbInsert.sql
 printf "INSERT INTO dbDb
     (name, description, nibPath, organism,
      defaultPos, active, orderKey, genome, scientificName,
      htmlPath, hgNearOk, hgPbOk, sourceName, taxId)
 VALUES\n" >> dbDbInsert.sql
 printf "(\"%s\", \"%s (%s/%s)\", \"/gbdb/%s\", \"%s\",
    \"%s\", 1, %d, \"%s\", \"%s\", \"/gbdb/%s/html/description.html\", 0,
      1, \"%s\", %d);\n" "${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