b87243c823ae619a0f382db4236df99216f3f1e8
braney
  Mon Dec 13 10:38:39 2021 -0800
some knownGene cleanup

diff --git src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM28.sh src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM28.sh
index 2e27324..921fa73 100644
--- src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM28.sh
+++ src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM28.sh
@@ -1,10 +1,19 @@
-screen -S knownGeneV39
+export db=mm39
+export GENCODE_VERSION=VM28
+export PREV_GENCODE_VERSION=VM27
+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":$PATH"
-cp /hive/data/genomes/hg38/bed/gencodeV38/build/buildEnv.sh  buildEnv.sh
+cp /hive/data/genomes/${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
 cp ${oldGeneDir}/${PREV_GENCODE_VERSION}.tables.txt  ${GENCODE_VERSION}.tables.txt
 
+hgsql ${oldKnownDb} -Ne "show tables"
+
 buildKnown.sh &