1390c194b5568d35616a26e699e56a0858e5aad2
hiram
  Fri May 28 13:43:15 2021 -0700
otto update scripts runnin in /hive/data/outside/ncbi/genomes/ncbiRefSeq refs #27553

diff --git src/hg/makeDb/doc/ncbiRefSeq/runUcscDb.sh src/hg/makeDb/doc/ncbiRefSeq/runUcscDb.sh
new file mode 100755
index 0000000..bb1bdb1
--- /dev/null
+++ src/hg/makeDb/doc/ncbiRefSeq/runUcscDb.sh
@@ -0,0 +1,43 @@
+#!/bin/bash
+
+set -beEu -o pipefail
+
+export TOP="/hive/data/outside/ncbi/genomes/ncbiRefSeq"
+cd "${TOP}"
+
+export db="$1"
+export Db="$2"
+export sumFile="$3"
+export asmId="$4"
+export wrkDir="$5"
+export gffFile="$6"
+
+srcSum=`md5sum "${gffFile}" | cut -d' ' -f1`
+prevSum=`cat ${sumFile}`
+
+if [ "${srcSum}" != "${prevSum}" ]; then
+exit 255
+  if [ ! -d "${wrkDir}" ]; then
+     mkdir "${wrkDir}"
+     cd "${wrkDir}"
+     printf "#!/bin/bash
+
+# otto script created by:
+#    /hive/data/outside/ncbi/genomes/ncbiRefSeq/ottoNcbiRefSeq.sh
+
+set -beEu -o pipefail
+cd $wrkDir
+~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=\`pwd\` \\
+      -bigClusterHub=ku -dbHost=hgwdev \\
+      -fileServer=hgwdev -smallClusterHub=hgwdev -workhorse=hgwdev \\
+      ${asmId} ${db}
+" > run.sh
+     chmod +x run.sh
+     time (./run.sh) > do.log 2>&1
+     cd "${TOP}"
+     printf "%s\n" "${srcSum}" > "${sumFile}"
+  fi
+else
+  printf "# $Db ncbiRefSeq is up to date\n" 1>&2
+fi
+