90ab34106679395529b254e024c8b0f350547195
braney
  Wed Nov 27 16:54:26 2019 -0800
add myGene2 link from hgGene on hg38

diff --git src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes20.sh src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes20.sh
index 88d9eaf..60dcc78 100755
--- src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes20.sh
+++ src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes20.sh
@@ -1114,15 +1114,25 @@
 
     rm -rf exonAA exonNuc
 
     export mz=multiz100way
     export gp=knownCanonical
     export db=hg38
     export pd=/usr/local/apache/htdocs-hgdownload/goldenPath/$db/$mz/alignments
     mkdir -p $pd
     rm -f $pd/$gp.exonAA.fa.gz
     rm -f $pd/$gp.exonNuc.fa.gz
     ln -s `pwd`/$gp.$mz.exonAA.fa.gz $pd/$gp.exonAA.fa.gz
     ln -s `pwd`/$gp.$mz.exonNuc.fa.gz $pd/$gp.exonNuc.fa.gz
     cd  $pd
     md5sum *.fa.gz > md5sum.txt
    
+
+#myGene2
+mkdir $dir/myGene2
+cd $dir/myGene2
+
+# copy list of genes from https://mygene2.org/MyGene2/genes 
+awk '{print $1}' | sort > genes.lst
+hgsql hg38 -Ne "select geneSymbol, kgId from kgXref" | sort > ids.txt
+join genes.lst  ids.txt | awk '{print $2,$1}' | sort > knownToMyGene2.txt
+hgLoadSqlTab $db knownToMyGene2 ~/kent/src/hg/lib/knownTo.sql knownToMyGene2.txt