be4311c07e14feb728abc6425ee606ffaa611a58
markd
  Fri Jan 22 06:46:58 2021 -0800
merge with master

diff --git src/hg/utils/otto/omim/checkOmim.sh src/hg/utils/otto/omim/checkOmim.sh
index 9d435fb..ef8e4d7 100755
--- src/hg/utils/otto/omim/checkOmim.sh
+++ src/hg/utils/otto/omim/checkOmim.sh
@@ -56,58 +56,58 @@
     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
+  #ln -s ../../doOmimPhenotype.pl ./doOmimPhenotype.pl
+  ln -s ../../doOmimPhenotypeNew ./doOmimPhenotypeNew
 
   ../../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
   done
 
   # archive the data
   if [ ! -d ${WORKDIR}/archive/${db} ]; then
     mkdir -p ${WORKDIR}/archive/${db}
   fi
   cd ${WORKDIR}/archive/${db}
-  mkdir ${today}
+  mkdir -p ${today}
   cd ${today}
   printf "This directory contains a backup of the OMIM track data tables built on %s\n" "${today}" > README 
   for i in `cat ${WORKDIR}/omim.tables`
   do
     hgsql --raw -Ne "show create table ${i}" ${db} > ${i}.sql
     hgsql -Ne "select * from ${i}" ${db} | gzip >  ${i}.txt.gz
   done
   cd ${WORKDIR}/${today}
   
 done
 
-
 rm -f "${WORKDIR}"/prev.md5sum.txt
 cp -p "${WORKDIR}/${today}"/md5sum.txt "${WORKDIR}"/prev.md5sum.txt
 echo "Omim Installed `date`" 
 
 else
     echo "No update `date` "
     cd "${WORKDIR}"
     rm -rf "${today}"
 fi