60ff056e1f85059922a4cb8532a9c8d1a7a7218d
braney
  Wed Aug 31 11:47:17 2022 -0700
update OMiM otto process to use ncbiRefSeq

diff --git src/hg/utils/otto/omim/makefile src/hg/utils/otto/omim/makefile
index 0d9bc13..65512eb 100644
--- src/hg/utils/otto/omim/makefile
+++ src/hg/utils/otto/omim/makefile
@@ -1,27 +1,27 @@
 SUBDIRS = doOmimGene2 doOmimGeneSymbols doOmimLocation
 PREFIX = /hive/data/outside/omim
 
 all: ${SUBDIRS:%=%.suball}
 FILES = omimWrapper.sh omim.tables checkOmim.sh validateOmim.sh parseGeneMap.pl omimUploadWrapper.sh checkOmimUpload.sh doOmimPhenotypeNew buildOmimTracks.sh flagOmimGene.py
 
 %.suball:
 	${MAKE} -C $* all
 
 # any changes must be committed (and this is checked).
 install: check-prefix installSub
-	cp omimWrapper.sh omim.tables checkOmim.sh validateOmim.sh parseGeneMap.pl omimUploadWrapper.sh checkOmimUpload.sh doOmimPhenotypeNew buildOmimTracks.sh flagOmimGene.py ${PREFIX}
+	cp doOmimGene2.sh omimWrapper.sh omim.tables checkOmim.sh validateOmim.sh parseGeneMap.pl omimUploadWrapper.sh checkOmimUpload.sh doOmimPhenotypeNew buildOmimTracks.sh flagOmimGene.py ${PREFIX}
 	cp ../../../lib/{omimGeneMap,omimGeneMap2,omim2gene,omimGeneSymbol,omimPhenotype,omimAv}.sql ${PREFIX}
 
 installSub: ${SUBDIRS:%=%.install}
 
 %.install:
 	${MAKE} -C $* install
 
 validate: check-prefix
 	$(foreach i, $(FILES), echo $(i); diff ${PREFIX}/$(i) $(i);)
 
 make-prefix: check-prefix
 	mkdir -p ${PREFIX}
 	mkdir -p ${PREFIX}/sql
 
 check-prefix: