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locks; strict;
comment	@# @;


1.3
date	2023.05.18.14.05.15;	author bacon;	state Exp;
branches;
next	1.2;
commitid	5x9aSLlLk5t62spE;

1.2
date	2017.12.17.14.30.36;	author bacon;	state Exp;
branches;
next	1.1;
commitid	bREpyF04m2L2KfjA;

1.1
date	2015.12.12.16.56.04;	author wiedi;	state Exp;
branches;
next	;
commitid	ZWCFwbSzmY7GdGMy;


desc
@@


1.3
log
@biology/bwa: Add support for aarch64 via devel/simde

May also work on other 64-bit architectures, but untested
@
text
@$NetBSD: patch-Makefile,v 1.2 2017/12/17 14:30:36 bacon Exp $

# Respect env, add librt for NetBSD

--- Makefile.orig	2017-10-23 17:10:17.000000000 +0000
+++ Makefile
@@@@ -1,6 +1,6 @@@@
-CC=			gcc
+CC?=			gcc
 #CC=			clang --analyze
-CFLAGS=		-g -Wall -Wno-unused-function -O2
+CFLAGS?=		-g -Wall -Wno-unused-function -O2
 WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
 AR=			ar
 DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
@@@@ -12,11 +12,14 @@@@ AOBJS=		bwashm.o bwase.o bwaseqio.o bwtg
 			bwtsw2_chain.o fastmap.o bwtsw2_pair.o
 PROG=		bwa
 INCLUDES=	
-LIBS=		-lm -lz -lpthread
+LDFLAGS+=	-lm -lz -lpthread
 SUBDIRS=	.
 
 ifeq ($(shell uname -s),Linux)
-	LIBS += -lrt
+	LDFLAGS += -lrt
+endif
+ifeq ($(shell uname -s),NetBSD)
+	LDFLAGS += -lrt
 endif
 
 .SUFFIXES:.c .o .cc
@@@@ -27,10 +30,10 @@@@ endif
 all:$(PROG)
 
 bwa:libbwa.a $(AOBJS) main.o
-		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@@ -L. -lbwa $(LIBS)
+		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@@ -L. -lbwa $(LDFLAGS)
 
 bwamem-lite:libbwa.a example.o
-		$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@@ -L. -lbwa $(LIBS)
+		$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@@ -L. -lbwa $(LDFLAGS)
 
 libbwa.a:$(LOBJS)
 		$(AR) -csru $@@ $(LOBJS)
@


1.2
log
@biology/bwa: Update to 0.7.17

Numerous bug fixes, enhancements, and new command-line options

ok wiz@@
@
text
@d1 3
a3 1
$NetBSD: patch-Makefile,v 1.1 2015/12/12 16:56:04 wiedi Exp $
a4 1
Respect env, add librt for NetBSD
@


1.1
log
@Fix int types and network libs on SunOS
@
text
@d1 1
a1 1
$NetBSD$
d3 2
a4 3
Don't overwrite pkgsrc CC and CFLAGS

--- Makefile.orig	2014-05-19 13:11:41.000000000 +0000
d8 1
a8 1
+#CC=			gcc
d11 1
a11 1
+#CFLAGS=		-g -Wall -Wno-unused-function -O2
d15 1
a15 1
@@@@ -11,7 +11,7 @@@@ AOBJS=		QSufSort.o bwt_gen.o bwase.o bwa
d20 1
a20 1
+LIBS=		-lm -lz -lpthread $(LDFLAGS)
d23 8
d32 13
@