src/hg/instinct/bioInt2/makefile 1.13

Index: src/hg/instinct/bioInt2/makefile
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/bioInt2/makefile,v
retrieving revision 1.12
retrieving revision 1.13
diff -b -B -U 1000000 -r1.12 -r1.13
--- src/hg/instinct/bioInt2/makefile	15 Jun 2009 17:45:24 -0000	1.12
+++ src/hg/instinct/bioInt2/makefile	1 Sep 2009 05:18:02 -0000	1.13
@@ -1,94 +1,94 @@
 include ../../../inc/common.mk
 
 L += $(MYSQLLIBS) -lm
 MYLIBDIR = ../../../lib/${MACHTYPE}
 MYLIBS = $(MYLIBDIR)/jkhmap.a $(MYLIBDIR)/jkhgap.a ${MYLIBDIR}/jkweb.a
 
 Gplusplus=g++
 
 #A1 = bioIntegrator
 #O1 = bioIntegrator.o bioIntDriver.o bioIntDb.o
 #H1 = bioIntDriver.h bioIntDb.h
 
 A2 = populateDb
 O2 = populateDb.o bioIntDb.o bioIntDriver.o createTables.o
 H2 = bioIntDb.h
 
 A3 = bioController
-O3 = bioController.o bioLevelI.o bioGeneLevel.o bioSetLevel.o bioPathwayLevel.o bioIntDriver.o bioIntDb.o createTables.o
+O3 = bioController.o bioLevelI.o bioGeneLevel.o bioSetLevel.o bioPathwayLevel.o bioPathwayLevelUsingEM.o bioIntDriver.o bioIntDb.o createTables.o
 H3 = bioIntDriver.h bioIntDb.h
 
 A4 = setCohorts
 O4 = setCohorts.o bioIntDb.o createTables.o
 H4 = bioIntDb.h
 
 A5 = cohortCorrelations
 O5 = cohortCorrelations.o bioIntDb.o createTables.o
 H5 = bioIntDb.h
 
 A6 = grabData
 O6 = grabData.o bioIntDb.o
 
 A7 = pathwayNullDist
 O7 = pathwayNullDist.o bioIntDb.o bioIntDriver.o createTables.o
 H7 = bioIntDriver.h bioIntDb.h
 
 A8 = makeClusterFiles
 O8 = makeClusterFiles.o bioIntDb.o bioIntDriver.o createTables.o
 H8 = bioIntDriver.h bioIntDb.h
 
 A = bioIntUI
 O = bioIntUI.o bioIntDb.o
 H = bioIntUI.h bioIntDb.h
 
 include ../../../inc/cgi_build_rules.mk
 
 HGFRONTEND = /usr/local/apache/htdocs/bioInt
 
 all: ${A1} ${A2} ${A3} ${A4} ${A} ${A5} ${A7}
 
 my::
 	rsync -a --exclude=CVS/ --delete bioIntFrontend/* ${HGFRONTEND}-${USER}/
 
 alpha::
 	rsync -rlD --exclude=CVS/ --delete bioIntFrontend/* ${HGFRONTEND}/
 
 compile: $O $H
 	${CC} ${COPT} $O ${MYLIBS} ${L}
 	mv ${AOUT} $A${EXE}
 
 bioIntUI: $O $H
 	${CC} ${COPT} $O ${MYLIBS} ${L}
 	mv ${AOUT} $A${EXE} 
 
 populateDb: ${O2} ${H2} ${MYLIBS}
 	${CC} ${COPT} ${O2} ${MYLIBS} ${L}
 	mv ${AOUT} ${A2}${EXE} 
 
 bioController: ${O3} ${H3}
 	${CC} ${COPT} ${O3} ${MYLIBS} ${L}
 	mv ${AOUT} ${A3}${EXE} 
 
 setCohorts: ${O4} ${H4}
 	${CC} ${COPT} ${O4} ${MYLIBS} ${L}
 	mv ${AOUT} ${A4}${EXE} 
 
 cohortCorrelations: ${O5} ${H5}
 	${CC} ${COPT} ${O5} ${MYLIBS} ${L}
 	mv ${AOUT} ${A5}${EXE} 
 
 grabData: ${O6}
 	${CC} ${COPT} ${O6} ${MYLIBS} ${L}
 	mv ${AOUT} ${A6}${EXE} 
 
 pathwayNullDist: ${O7} ${H7}
 	${CC} ${COPT} ${O7} ${MYLIBS} ${L}
 	mv ${AOUT} ${A7}${EXE} 
 
 makeClusterFiles: ${O8} ${H8}
 	${CC} ${COPT} ${O8} ${MYLIBS} ${L}
 	mv ${AOUT} ${A8}${EXE} 
 
 clean::
 	rm -f ${O1} ${O2} ${O3} ${O4} ${O}