bwa: Fix CentOS build, generate plist

[Jason Bacon <bacon4000%gmail.com@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Thu Dec 14 09:26:16 2017 -0600
Changeset:	085ba1393a8c2d6dc0e5f1aad529f2e62148683b

Modified Files:
	bwa/PLIST
	bwa/distinfo
	bwa/patches/patch-Makefile

Log Message:
bwa: Fix CentOS build, generate plist

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=085ba1393a8c2d6dc0e5f1aad529f2e62148683b

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 bwa/PLIST                  |  4 ++++
 bwa/distinfo               |  2 +-
 bwa/patches/patch-Makefile | 30 +++++++++++++++++++++++++-----
 3 files changed, 30 insertions(+), 6 deletions(-)

diffs:
diff --git a/bwa/PLIST b/bwa/PLIST
index 48d96a5493..7ca657864f 100644
--- a/bwa/PLIST
+++ b/bwa/PLIST
@@ -1 +1,5 @@
 @comment $NetBSD$
+bin/bwa
+bin/qualfa2fq.pl
+bin/xa2multi.pl
+man/man1/bwa.1
diff --git a/bwa/distinfo b/bwa/distinfo
index eef9dfc3c8..1f95203bfa 100644
--- a/bwa/distinfo
+++ b/bwa/distinfo
@@ -4,4 +4,4 @@ SHA1 (bwa-0.7.17.tar.gz) = 77f9aac723110227ea51cb42011336d291d03723
 RMD160 (bwa-0.7.17.tar.gz) = d26a266387dee4fc9fcf6eef4f7ffcc076495c22
 SHA512 (bwa-0.7.17.tar.gz) = 114e61b7cc5edcb67172d1eca7be1fa670ea33dd48b5c02c98318e254871363775c0dab327fd7ee7023200a5fedc745fa01cbe0fd9550d783f091d4df6926f48
 Size (bwa-0.7.17.tar.gz) = 232593 bytes
-SHA1 (patch-Makefile) = 34e807355fc8f431214f0b1c7be5ed524fe0f620
+SHA1 (patch-Makefile) = ae66ec8b80c03c2f5a54924d21e1fe3b9bb3e004
diff --git a/bwa/patches/patch-Makefile b/bwa/patches/patch-Makefile
index 49d7a2cf84..b86e7e9f6e 100644
--- a/bwa/patches/patch-Makefile
+++ b/bwa/patches/patch-Makefile
@@ -12,13 +12,33 @@ $NetBSD$
  WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
  AR=			ar
  DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
-@@ -18,6 +18,9 @@ SUBDIRS=	.
+@@ -12,11 +12,14 @@ AOBJS=		bwashm.o bwase.o bwaseqio.o bwtg
+ 			bwtsw2_chain.o fastmap.o bwtsw2_pair.o
+ PROG=		bwa
+ INCLUDES=	
+-LIBS=		-lm -lz -lpthread
++LDFLAGS+=	-lm -lz -lpthread
+ SUBDIRS=	.
+ 
  ifeq ($(shell uname -s),Linux)
- 	LIBS += -lrt
- endif
-+ifeq ($(shell uname -s),NetBSD)
-+	LIBS += -lrt
+-	LIBS += -lrt
++	LDFLAGS += -lrt
 +endif
++ifeq ($(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)