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
@@ -1,96 +1,97 @@
 #!/bin/sh -e
 
 #	Do not modify this script, modify the source tree copy:
 #	src/hg/utils/omim/checkOmim.sh
 
 # set EMAIL here for notification list
 #EMAIL="braney@soe.ucsc.edu"
 # set DEBUG_EMAIL here for notification of potential errors in the process
 #DEBUG_EMAIL="braney@soe.ucsc.edu"
 
 #	cron jobs need to ensure this is true
 umask 002
 
 WORKDIR=$1
 export WORKDIR
 export PATH=$WORKDIR":$PATH"
 
 #	this is where we are going to work
 if [ ! -d "${WORKDIR}" ]; then
     echo "ERROR in OMIM release watch, Can not find the directory:     ${WORKDIR}" 
     exit 255
 fi
 
 cd "${WORKDIR}"
 
 
 ######################
 # Checking if there's a new release
 
 today=`date +%F`
 mkdir -p $today
 cd $today
 
 # fetch remote files
 echo fetching files ...
 wget -nv -i ../omimUrls.txt -o wget.log
 if [ $? -ne 0 ]; then
     echo "Potential error in OMIM release fetch,
 check wget.log in ${WORKDIR}/${today}"
     exit 255
 fi
 
 ls | grep -v wget.log | xargs -I % sh -c "echo -ne '%\t'; (grep -v '^#' % || true) | md5sum | awk '{print \$1}'" | sort > md5sum.txt
 
 if [ ! -e ../prev.md5sum.txt ]
 then
     touch ../prev.md5sum.txt
 fi
 
 diff md5sum.txt ../prev.md5sum.txt > release.diff || true
 
 WC=`cat release.diff | wc -l`
 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
   done
 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