10fb7902ebfda7cdddb0b410d506bf2f571b4ec6
jcasper
  Wed Jul 15 21:20:24 2026 -0700
TrackDb and makedoc for UCSC Genes version of GENCODE VM39, refs #37391

diff --git src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM39.sh src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM39.sh
new file mode 100644
index 00000000000..fe02c0d670d
--- /dev/null
+++ src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM39.sh
@@ -0,0 +1,53 @@
+# Jonathan - began 2025-09-16
+
+export db=mm39
+export GENCODE_VERSION=VM39
+export PREV_GENCODE_VERSION=VM38
+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 .
+
+cp ${oldGeneDir}/${PREV_GENCODE_VERSION}.tables.txt .
+
+hgsql ${oldKnownDb} -Ne "show tables" > ${oldKnownDb}.tables.txt
+diff <(sort ${PREV_GENCODE_VERSION}.tables.txt) <(sort ${oldKnownDb}.tables.txt)
+# no difference
+
+buildKnown.sh &
+# wait for completion
+# hiccups with RNAfold in some FoldUtr steps - had to upgrade RNAfold version
+
+tail -n 1 *.log
+# ==> doBioCyc.log <==
+# BuildBioCyc successfully finished
+#
+# ==> doBlast.log <==
+# BuildBlast successfully finished
+#
+# ==> doFoldUtr.log <==
+# BuildFoldUtr successfully finished
+#
+# ==> doKnown.log <==
+# BuildKnown successfully finished
+#
+# ==> doKnownTo.log <==
+# BuildKnownTo successfully finished
+#
+# ==> doPfamScop.log <==
+# BuildPfamScop successfully finished
+
+# Manual GTF step
+cd /hive/data/genomes/$db/goldenPath/bigZips/genes
+genePredToGtf -utr ${tempDb} knownGene ${db}.knownGene.gtf
+rm -f ${db}.knownGene.gtf.gz
+gzip ${db}.knownGene.gtf
+cd $dir
+