c8c1b1a9adac6dfa7a869326ca3f774a724a50db
lrnassar
  Fri Sep 4 17:51:48 2026 -0700
Document the RefSeq Historical protein table build and add a reminder to the notifier.

The historical rna.gbff we already download carries a /translation for every
coding record, and gbProcess has a -pepFa flag that writes them out, so this is
one extra pass over a file we have rather than a new download. Adds the build
steps to the RS_2024_08 makedoc section, and two lines to the weekly notifier so
the next refresh does not leave the protein table behind. refs #38248

diff --git src/hg/utils/otto/refSeqHistorical/checkRefSeqHistoricalUpdate.sh src/hg/utils/otto/refSeqHistorical/checkRefSeqHistoricalUpdate.sh
index e00b04aadb4..1ea39964e98 100755
--- src/hg/utils/otto/refSeqHistorical/checkRefSeqHistoricalUpdate.sh
+++ src/hg/utils/otto/refSeqHistorical/checkRefSeqHistoricalUpdate.sh
@@ -30,18 +30,20 @@
     exit 1
 fi
 
 latest=$(echo "$listing" | grep -oE 'RS_[0-9]{4}_[0-9]{2}' | sort -u | tail -1)
 if [ -z "$latest" ]; then
     echo "refSeqHistorical check: no RS_* release tags found at $baseUrl (page format changed?)"
     exit 1
 fi
 
 if [[ "$latest" > "$handled" ]]; then
     echo "New RefSeq historical release available for hg38: $latest (we have: ${handled:-none})"
     echo "Source: $baseUrl"
     echo "Build steps: RS_YYYY_MM section in kent/src/hg/makeDb/doc/hg38/ncbiRefSeq.txt"
     echo "Do not forget /gbdb/hg38/ncbiRefSeq/ncbiRefSeqHistoricalVersion.txt, the"
     echo "track's own version string -- last step of that makedoc section."
+    echo "Also rebuild ncbiRefSeqPepTableHistorical (the gbProcess -pepFa step)"
+    echo "or HGVS protein terms on newly deprecated accessions will not resolve."
     echo "To silence: set $latest in /hive/data/outside/otto/refSeqHistorical/lastHandledRelease.txt. refs #35766"
 fi
 exit 0