c18e69d83c6e7c80bae078cc840389a88e7eafc5
jcasper
  Thu Apr 4 11:40:26 2024 -0700
Correcting minor typos for knownGeneV45, refs #32414

diff --git src/hg/makeDb/doc/ucscGenes/hg38.gencodeV45.sh src/hg/makeDb/doc/ucscGenes/hg38.gencodeV45.sh
index 7228638..dd6f7d2 100644
--- src/hg/makeDb/doc/ucscGenes/hg38.gencodeV45.sh
+++ src/hg/makeDb/doc/ucscGenes/hg38.gencodeV45.sh
@@ -1,33 +1,33 @@
 export db=hg38
-export GENCODE_VERSION=V44
-export PREV_GENCODE_VERSION=V43
+export GENCODE_VERSION=V45
+export PREV_GENCODE_VERSION=V44
 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
 
 # NB: Had to manually construct the files.txt file; it was missing.
 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 &
 
 # After that's done, then can do the myGene2 knownTo (hasn't been integrated because it needs
 # manual gene list fetch).
 #myGene2
 mkdir $dir/myGene2
 cd $dir/myGene2
 
 # copy list of genes to a file from https://mygene2.org/MyGene2/genes
 awk '{print $1}' thatfile | sort > genes.lst
 hgsql hg38 -Ne "select geneSymbol, kgId from kgXref" | sort > ids.txt
 join -t $'\t' genes.lst  ids.txt | tawk '{print $2,$1}' | sort > knownToMyGene2.txt
 hgLoadSqlTab $db knownToMyGene2 ~/kent/src/hg/lib/knownTo.sql knownToMyGene2.txt