d2da1341d245cf5a5d574e2f75375ef49091ad30
chmalee
  Tue Jul 16 13:18:35 2019 -0700
Rework of omim otto pipeline to accomadate new genemap schema, no refs

diff --git src/hg/utils/otto/omim/checkOmim.sh src/hg/utils/otto/omim/checkOmim.sh
index 13e4693..160809f 100755
--- src/hg/utils/otto/omim/checkOmim.sh
+++ src/hg/utils/otto/omim/checkOmim.sh
@@ -53,30 +53,31 @@
 if [ "${WC}" -gt 0 ]; then
 #####################
 # There's a new release!
     echo -e "New OMIM update noted at:\n" \
 "http://omim.org/\n"`comm -13 ../prev.md5sum.txt md5sum.txt`"/" 
 
 # build the new OMIM track tables for hg18, hg19, hg38
 for db in hg18 hg19 hg38
 do
   echo Running OMIM build for $db
   rm -rf $db
   mkdir -p $db
   cd $db
 
   ln -s ../genemap.txt ./genemap.txt
+  ln -s ../genemap2.txt ./genemap2.txt
   ln -s ../allelicVariants.txt ./allelicVariants.txt
   ln -s ../mim2gene.txt ./mim2gene.txt
   ln -s ../../doOmimPhenotype.pl ./doOmimPhenotype.pl
 
   ../../buildOmimTracks.sh $db
   ../../flagOmimGene.py $db > omimGene2.prev.flagged
   ../../validateOmim.sh $db
   cd ..
 
   # install new tables
   for table in `cat ../omim.tables`
   do 
     new=$table"New"
     old=$table"Old"
     hgsqlSwapTables $db $new $table $old -dropTable3