6eed61012da9293c065a6b0f901a4f7c70ddb215
jcasper
  Tue Aug 22 13:30:08 2023 -0700
makedoc for GENCODE VM33 knownGene build, refs #30841

diff --git src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM33.sh src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM33.sh
new file mode 100644
index 0000000..61c71aa
--- /dev/null
+++ src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM33.sh
@@ -0,0 +1,47 @@
+export db=mm39
+export GENCODE_VERSION=VM33
+export PREV_GENCODE_VERSION=VM32
+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  ${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  ${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 <==
+# BuildKnownTo successfully finished
+#
+# ==> doPfamScop.log <==
+# BuildPfamScop successfully finished
+
+# build completed.
+
+