From b4649db619f8514efb9377422de3ea42154b3a80 Mon Sep 17 00:00:00 2001
From: Ted Tanberry <ted.tanberry@gmail.com>
Date: Thu, 5 Feb 2015 20:20:03 +0100
Subject: Updated bwa to 0.7.12 and modernized the build system. Removed
 hard-coded ar.

---
 sci-biology/bwa/files/bwa_Makefile.patch | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 sci-biology/bwa/files/bwa_Makefile.patch

(limited to 'sci-biology/bwa/files')

diff --git a/sci-biology/bwa/files/bwa_Makefile.patch b/sci-biology/bwa/files/bwa_Makefile.patch
new file mode 100644
index 000000000..406e9b052
--- /dev/null
+++ b/sci-biology/bwa/files/bwa_Makefile.patch
@@ -0,0 +1,27 @@
+--- Makefile
++++ Makefile
+@@ -1,8 +1,8 @@
+-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
++AR?=			ar
+ DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
+ LOBJS=		utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o
+ AOBJS=		QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
+@@ -26,10 +26,10 @@
+ all:$(PROG)
+ 
+ bwa:libbwa.a $(AOBJS) main.o
+-		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
++		$(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
+ 
+ bwamem-lite:libbwa.a example.o
+-		$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
++		$(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
+ 
+ libbwa.a:$(LOBJS)
+ 		$(AR) -csru $@ $(LOBJS)
-- 
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