src/hg/tcga/bamToFastQ/makefile 1.2

Index: src/hg/tcga/bamToFastQ/makefile
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/tcga/bamToFastQ/makefile,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/tcga/bamToFastQ/makefile	9 Mar 2010 23:25:57 -0000	1.1
+++ src/hg/tcga/bamToFastQ/makefile	10 Mar 2010 00:21:31 -0000	1.2
@@ -1,23 +1,29 @@
 USE_BAM = 1
 include ../../../inc/common.mk
 
 L += $(MYSQLLIBS) -lm
 MYLIBDIR = ../../../lib/${MACHTYPE}
 MYLIBS =  $(MYLIBDIR)/jkhgap.a ${MYLIBDIR}/jkweb.a
 
+# libbam, will need to change SAMDIR to where it is on your system
+SAMDIR = /cluster/home/jsanborn/samtools
+SAMINC = ${SAMDIR}
+SAMLIB = ${SAMDIR}/libbam.a
+
 ifeq (${USE_BAM},1)
     MYLIBS += ${SAMLIB}
 endif
 
+
 A = bamToFastQ
 O = bamToFastQ.o
 
 bamToFastQ: ${O} ${MYLIBS}
 	${CC} ${COPT} -o ${DESTDIR}${BINDIR}/${A}${EXE} $O ${MYLIBS} $L
 	${STRIP} ${DESTDIR}${BINDIR}/${A}${EXE}
 
 compile:: ${O}
 	${CC} ${COPT} -o ${A}${EXE} ${O} ${MYLIBS} $L
 
 clean::
 	rm -f ${A} ${O}