bfb6267a05fde313f64ae853a48b8d07f5d48316
jcasper
  Fri Aug 23 17:16:14 2024 -0700
Makedoc for knownGeneV47lift37, refs #34226

diff --git src/hg/makeDb/doc/ucscGenes/hg19.gencodeV47lift37.sh src/hg/makeDb/doc/ucscGenes/hg19.gencodeV47lift37.sh
new file mode 100644
index 0000000..6f69292
--- /dev/null
+++ src/hg/makeDb/doc/ucscGenes/hg19.gencodeV47lift37.sh
@@ -0,0 +1,27 @@
+export db=hg19
+export GENCODE_VERSION=V47lift37
+export PREV_GENCODE_VERSION=V45lift37
+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
+
+# files didn't exist; created it based on a template from V47 on hg38
+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 ${oldKnownDb}.tables.txt)
+# no difference
+
+buildKnown.sh &
+
+# Continue with the steps to load the tables into the database.
+
+# make sure knownGeneOld${PREV_GENCODE_VERSION} is populated with the previous knownGene
+# contents, and that the track and HTML page are updated accordingly.  This step should be
+# obsolete soon.