339f301a906608e65e98d494054ef975a5b68f44
braney
  Thu Feb 10 12:43:04 2022 -0800
take Lynx out of knownGene build

diff --git src/hg/utils/otto/knownGene/buildTo.sh src/hg/utils/otto/knownGene/buildTo.sh
index 577d9d1..0edf72a 100755
--- src/hg/utils/otto/knownGene/buildTo.sh
+++ src/hg/utils/otto/knownGene/buildTo.sh
@@ -9,37 +9,37 @@
 hgMapToGene -geneTableType=genePred -tempDb=$tempDb $db ncbiRefSeq knownGene knownToLocusLink -lookup=refToLl.txt
 rm refToLl.txt
 
 if test "$gtexGeneMode" != ""
 then
     hgMapToGene -geneTableType=genePred $db -tempDb=$tempDb -all -type=genePred $gtexGeneMode knownGene knownToGtex
 fi
 
 # knownToEnsembl and knownToGencode${GENCODE_VERSION}
 awk '{OFS="\t"} {print $4,$4}' ucscGenes.bed | sort | uniq > knownToEnsembl.tab
 cp knownToEnsembl.tab knownToGencode${GENCODE_VERSION}.tab
 hgLoadSqlTab -notOnServer $tempDb  knownToEnsembl  $kent/src/hg/lib/knownTo.sql  knownToEnsembl.tab
 hgLoadSqlTab -notOnServer $tempDb  knownToGencode${GENCODE_VERSION}  $kent/src/hg/lib/knownTo.sql  knownToGencode${GENCODE_VERSION}.tab
 
 # make knownToLynx
-wget "http://lynx.ci.uchicago.edu/downloads/LYNX_GENES.tab"
-awk '{print $2}' LYNX_GENES.tab | sort > lynxExists.txt
-hgsql -e "select geneSymbol,kgId from kgXref" --skip-column-names $tempDb | awk '{if (NF == 2) print}' | sort > geneSymbolToKgId.txt
-join lynxExists.txt geneSymbolToKgId.txt | awk 'BEGIN {OFS="\t"} {print $2,$1}' | sort > knownToLynx.tab
-hgLoadSqlTab -notOnServer $tempDb  knownToLynx $kent/src/hg/lib/knownTo.sql  knownToLynx.tab
+#wget "http://lynx.ci.uchicago.edu/downloads/LYNX_GENES.tab"
+#awk '{print $2}' LYNX_GENES.tab | sort > lynxExists.txt
+#hgsql -e "select geneSymbol,kgId from kgXref" --skip-column-names $tempDb | awk '{if (NF == 2) print}' | sort > geneSymbolToKgId.txt
+#join lynxExists.txt geneSymbolToKgId.txt | awk 'BEGIN {OFS="\t"} {print $2,$1}' | sort > knownToLynx.tab
+#hgLoadSqlTab -notOnServer $tempDb  knownToLynx $kent/src/hg/lib/knownTo.sql  knownToLynx.tab
 
-rm lynxExists.txt geneSymbolToKgId.txt
+#rm lynxExists.txt geneSymbolToKgId.txt
 
 # load malacards table
 if test "$malacardTable" != ""
 then
     hgsql -e "select geneSymbol,kgId from kgXref" --skip-column-names $tempDb | awk '{if (NF == 2) print}' | sort > geneSymbolToKgId.txt
     hgsql -e "select geneSymbol from malacards" --skip-column-names $db | sort > malacardExists.txt
     join malacardExists.txt  geneSymbolToKgId.txt | awk 'BEGIN {OFS="\t"} {print $2, $1}' > knownToMalacard.txt
     hgLoadSqlTab -notOnServer $tempDb  knownToMalacards $kent/src/hg/lib/knownTo.sql  knownToMalacard.txt
     rm geneSymbolToKgId.txt malacardExists.txt knownToMalacard.txt
 fi
 
 #knownToVisiGene
 knownToVisiGene $tempDb -probesDb=$db
 
 hgsql $tempDb -e "select geneSymbol,name from knownGene g, kgXref x where g.name=x.kgId " | sort > $tempDb.symbolToId.txt