a7b8d7430248b2898d2f79c40a49665b06c033c1
hiram
  Tue Oct 19 14:00:23 2021 -0700
scripts to run the NCBI RefSeq update automatically refs #24735

diff --git src/hg/utils/otto/ncbiRefSeq/archiveOne.sh src/hg/utils/otto/ncbiRefSeq/archiveOne.sh
new file mode 100755
index 0000000..c92792e
--- /dev/null
+++ src/hg/utils/otto/ncbiRefSeq/archiveOne.sh
@@ -0,0 +1,40 @@
+#!/bin/bash
+
+set -beEu -o pipefail
+
+if [ $# -ne 1 ]; then
+  printf "usage: archiveOne.sh <wrkDir>\n" 1>&2
+  printf "where <wrkDir> is something like:\n\t/hive/data/genomes/hg38/bed/ncbiRefSeq.p13.2021-05-28\n" 1>&2
+  exit 255
+fi
+
+export wrkDir=$1
+export db=`echo $wrkDir | cut -d'/' -f5`
+export version=`awk '{print $(NF-1)}' ${wrkDir}/process/ncbiRefSeqVersion.txt`
+export dumpDir="${wrkDir}/archive"
+export arkDir="/usr/local/apache/htdocs-hgdownload/goldenPath/archive/$db/ncbiRefSeq/$version"
+
+printf "#      db: %s\n" "${db}" 1>&2
+printf "# version: %s\n" "${version}" 1>&2
+printf "#  arkDir: %s\n" "${arkDir}" 1>&2
+printf "# dumpDir: %s\n" "${dumpDir}" 1>&2
+
+mkdir -p "${dumpDir}"
+
+for tbl in extNcbiRefSeq ncbiRefSeq ncbiRefSeqCds ncbiRefSeqCurated \
+	ncbiRefSeqLink ncbiRefSeqOther ncbiRefSeqPepTable ncbiRefSeqPsl \
+	seqNcbiRefSeq ncbiRefSeqHgmd ncbiRefSeqSelect
+do
+  printf "# %s.%s\n" "${db}" "${tbl}" 1>&2
+  hgsqldump --no-data "${db}" "${tbl}" > "${dumpDir}/${db}.${tbl}.sql"
+  hgsql -N "${db}" -e "select * from ${tbl};" | gzip -c > "${dumpDir}/${db}.${tbl}.txt.gz"
+done
+
+for file in ncbiRefSeqOther.bb ncbiRefSeqOther.ix ncbiRefSeqOther.ixx \
+        ncbiRefSeqVersion.txt seqNcbiRefSeq.rna.fa ncbiRefSeqGenomicDiff.bb
+do
+  printf "# gbdb %s %s\n" "${db}" "${file}" 1>&2
+  cp -p "/gbdb/${db}/ncbiRefSeq/${file}" "${dumpDir}/gbdb.${db}.${file}"
+done
+printf "# gzip gbdb.%s.seqNcbiRefSeq.rna.fa\n" "${db}" 1>&2
+gzip "${dumpDir}/gbdb.${db}.seqNcbiRefSeq.rna.fa"