src/hg/pslPseudo/makefile 1.15

Index: src/hg/pslPseudo/makefile
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/pslPseudo/makefile,v
retrieving revision 1.14
retrieving revision 1.15
diff -b -B -U 1000000 -r1.14 -r1.15
--- src/hg/pslPseudo/makefile	21 Feb 2008 02:13:23 -0000	1.14
+++ src/hg/pslPseudo/makefile	10 Mar 2009 00:34:29 -0000	1.15
@@ -1,55 +1,55 @@
 include ../../inc/common.mk
 
 
-L = -lm $(MYSQLLIBS)
+L += -lm $(MYSQLLIBS)
 MYLIBDIR = ../../lib/$(MACHTYPE)
 MYLIBS =  $(MYLIBDIR)/jkhgap.a $(MYLIBDIR)/jkweb.a 
 DEBUGOPTIONS = -skipExciseRepeats -minAli=0.98 -nearTop=0.005 
 OPTIONS = -minAli=0.98 -nearTop=0.005 -verbose=3 -stripVersion
 #MARKDEBUG = /cse/grads/markd/compbio/dbgmalloc/debug-malloc.o
 MARKDEBUG =
 DB = hg17
 MRNA = mrnaHg17.2bit 
 DBDIR = /cluster/data/$(DB)
 BED = $(DBDIR)/bed
 PSEUDO = $(DBDIR)/bed/pseudo
 BUILD=gs.17/build34
 VALCMD = chr13.sizes ${PSEUDO}/rmsk.bed $(PSEUDO)/chr13mouseSyn.bed $(PSEUDO)/chr13simple.bed $(PSEUDO)/chr13_mrna.psl 
 TESTCMD = $(DBDIR)/chrom.sizes ${PSEUDO}/rmsk.bed.gz $(PSEUDO)/mouseNet.txt $(PSEUDO)/dogNet.txt $(BED)/simpleRepeat/simpleRepeat.bed $(PSEUDO)/all_mrna.psl 
 #TESTCMD = $(DBDIR)/chrom.sizes mtRmsk mtSyn.bed mtSimple.bed input/test48.psl
 GENES = $(PSEUDO)/refGene.tab $(PSEUDO)/mgcGene.tab $(PSEUDO)/sortedKnownGene.tab
 
 
 O = pslPseudo.o 
 
 pslPseudo: $O $(MYLIBS)
 	gcc -ggdb -o ${BINDIR}/pslPseudo $O $(MARKDEBUG) $(MYLIBS) $L 
 	#${STRIP} ${BINDIR}/pslPseudo${EXE}
 
 lib:
 	cd ../../lib && ${MAKE}
 	cd ../lib && ${MAKE}
 
 test: test1 test2 test3 test4 test5 test6 test7 test8 test9 test10 test13 test14 test15 test16 test17 test18 test19 testRp131 test26 test38
 %:	inputHg17/%.psl
 	${MKDIR} output
 	MALLOC_LOG=malloc.log MALLOC_LOG_OPTS=SAD pslPseudo $(OPTIONS) $(DB) inputHg17/$@.psl $(TESTCMD)  output/$@g.psl output/$@p.psl output/$@l.txt output/$@.axt S1.hg17.lst $(MRNA) $(GENES) > $@.log 2> $@.err
 	diff expected/$@g.psl output/$@g.psl 
 	diff expected/$@p.psl output/$@p.psl | awk '{print $$15":"$$17"-"$$18}'
 	diff expected/$@p.psl output/$@p.psl
 #	rm output/$@g.psl output/$@p.psl
 #test48:	input/test1.psl
 #	${MKDIR} output
 #	pslPseudo $(OPTIONS) $(DB) input/$@.psl $(TESTCMD)  output/$@g.psl output/$@p.psl output/$@l.txt output/$@.axt S1.lst AF387618.fa $(GENES)  
 #	diff expected/$@g.psl output/$@g.psl 
 #	diff expected/$@p.psl output/$@p.psl
 ##	rm output/$@g.psl output/$@p.psl
 #jtest59:	input/test59.psl
 #j	${MKDIR} output
 #j	MALLOC_LOG=malloc.log MALLOC_LOG_OPTS=SAD  pslPseudo $(OPTIONS) $(DB) input/$@.psl $(VALCMD)  output/$@g.psl output/$@p.psl output/$@l.txt output/$@.axt S1.lst mrnaHg16.fa $(GENES) 2> valgrind.out > test59.log
 #valgrind -v --leak-resolution=high --leak-check=yes --num-callers=25 --show-reachable=yes pslPseudo $(OPTIONS) $(DB) input/$@.psl $(VALCMD)  output/$@g.psl output/$@p.psl output/$@l.txt output/$@.axt S1.lst mrnaHg16.fa $(GENES) 2> valgrind.out
 	diff expected/$@g.psl output/$@g.psl 
 	diff expected/$@p.psl output/$@p.psl
 
 clean:
 	rm -fr ${O} output