e84397db43e064ebc8fb853773d1e48fbdc7aa46
jcasper
  Wed Mar 6 10:43:19 2024 -0800
Makedoc for knownGeneVM34, refs #32415

diff --git src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM34.sh src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM34.sh
new file mode 100644
index 0000000..7da9127
--- /dev/null
+++ src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM34.sh
@@ -0,0 +1,56 @@
+# Jonathan - began 2024-02-26
+
+export db=mm39
+export GENCODE_VERSION=VM34
+export PREV_GENCODE_VERSION=VM33
+screen -S knownGene${GENCODE_VERSION}
+mkdir /hive/data/genomes/$db/bed/gencode$GENCODE_VERSION/build
+cd /hive/data/genomes/$db/bed/gencode$GENCODE_VERSION/build
+
+PATH=$HOME/kent/src/hg/utils/otto/knownGene":$PATH"
+cp /hive/data/genomes/${db}/bed/gencode${PREV_GENCODE_VERSION}/build/buildEnv.sh  buildEnv.sh
+
+# edit buildEnv.sh
+ . buildEnv.sh
+
+cp ${oldGeneDir}/${PREV_GENCODE_VERSION}.files.txt .
+# This failed on account of the V32 file was missing.  I reconstructed it and the V33 version by hand.
+
+cp ${oldGeneDir}/${PREV_GENCODE_VERSION}.tables.txt .
+
+hgsql ${oldKnownDb} -Ne "show tables" > ${oldKnownDb}.tables.txt
+diff <(sort ${PREV_GENCODE_VERSION}.tables.txt) <(sort ${oldKnownDb}.tables.txt)
+# no difference
+
+buildKnown.sh &
+# wait for completion
+
+tail -n 1 *.log
+# ==> doBioCyc.log <==
+# BuildBioCyc successfully finished
+#
+# ==> doBlast.log <==
+# BuildBlast successfully finished
+#
+# ==> doFoldUtr.log <==
+# BuildFoldUtr successfully finished
+#
+# ==> doKnown.log <==
+# BuildKnown successfully finished
+#
+# ==> doKnownTo.log <==
+# Expecting 2 words line 136223 of refToLl.txt got 1.
+#
+# ==> doPfamScop.log <==
+# BuildPfamScop successfully finished
+
+# So something went wrong with doKnownTo.
+# Turned out it was because ncbiRefSeqLink now has records without locusLinkId
+# populated, which was unexpected.  Since LocusLink is now discontinued, we'll
+# have to look into what purpose this still serves.  Skipping over those
+# records for now was enough to permit completion.
+# The build is now finished.
+
+# Current next steps: Adding IsPcr server, double check all.joiner, check in logs,
+# update tickets & tables. (all in knownGene build wiki page).  Then do post-release
+# "push other species" blast tables