1 files changed, 25 insertions, 18 deletions
diff --git a/biology/phrap/files/patch-makefile b/biology/phrap/files/patch-makefile
index 7fccdb3846a1..2a83cd9e1e44 100644
--- a/biology/phrap/files/patch-makefile
+++ b/biology/phrap/files/patch-makefile
@@ -1,9 +1,9 @@
---- makefile.orig	1999-03-11 15:13:20.000000000 +0900
-+++ makefile	2007-12-11 13:19:39.000000000 +0900
-@@ -23,8 +23,8 @@
- #*****************************************************************************/
- 
+--- ./makefile.orig	2009-06-02 17:45:34.000000000 +0200
++++ ./makefile	2014-08-02 12:43:45.000000000 +0200
+@@ -25,8 +25,8 @@
  # Makefile for swat, phrap, cross_match, phrapview; also swprobs (currently inactivated)
+ #CC= icc
+ #CFLAGS= -O2 -wd266,880
 -CC= cc
 -CFLAGS= -O2
 +CC?= cc
@@ -11,17 +11,24 @@
  LFLAGS= -lm
  
  SWATOBJS= swat.o weibull.o
-@@ -55,11 +55,11 @@
+@@ -55,7 +55,7 @@
+ 
+ CALFOBJS= calf_merge.o  calf_utils.o
+ 
+-all:  swat phrap cross_match phrapview cluster loco calf_merge
++all:  swat phrap cross_match phrapview pcluster loco calf_merge
+ 
+ #manyreads:  
+ #	touch swat.h;
+@@ -131,9 +131,9 @@
+ 	$(CC) $(CFLAGS) -o $@ gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LFLAGS)
+ 	chmod o-r gccross_match
+ 
+-cluster: makefile $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS)
++pcluster: makefile $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS)
+ 	$(CC) $(CFLAGS) -o $@ $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) $(LFLAGS)
+-	chmod o-r cluster
++	chmod o-r pcluster
  
- manyreads:  
- 	touch swat.h;
--	make CFLAGS="-O2 -DMANYREADS" phrap cross_match;
-+	make CFLAGS="$(CFLAGS) -DMANYREADS" phrap cross_match;
- 	mv phrap phrap.manyreads;
- 	mv cross_match cross_match.manyreads;
- 	touch swat.h;
--	make CFLAGS="-O2 -DLONGREADS" phrap;
-+	make CFLAGS="$(CFLAGS) -DLONGREADS" phrap;
- 	mv phrap phrap.longreads;
- 	touch swat.h;
- 	make phrap cross_match;
+ loco: makefile $(LOCOOBJS) $(SWOBJS)
+ 	$(CC) $(CFLAGS) -o $@ $(LOCOOBJS) $(SWOBJS) $(LFLAGS)