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CVS commit: pkgsrc/biology/bwa
Module Name: pkgsrc
Committed By: bacon
Date: Sun Dec 17 14:30:36 UTC 2017
Modified Files:
pkgsrc/biology/bwa: Makefile distinfo
pkgsrc/biology/bwa/patches: patch-Makefile
Removed Files:
pkgsrc/biology/bwa/patches: patch-kopen.c
Log Message:
biology/bwa: Update to 0.7.17
Numerous bug fixes, enhancements, and new command-line options
ok wiz@
To generate a diff of this commit:
cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/bwa/Makefile \
pkgsrc/biology/bwa/distinfo
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/bwa/patches/patch-Makefile
cvs rdiff -u -r1.1 -r0 pkgsrc/biology/bwa/patches/patch-kopen.c
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
Modified files:
Index: pkgsrc/biology/bwa/Makefile
diff -u pkgsrc/biology/bwa/Makefile:1.4 pkgsrc/biology/bwa/Makefile:1.5
--- pkgsrc/biology/bwa/Makefile:1.4 Sat Jul 9 06:37:51 2016
+++ pkgsrc/biology/bwa/Makefile Sun Dec 17 14:30:36 2017
@@ -1,13 +1,11 @@
-# $NetBSD: Makefile,v 1.4 2016/07/09 06:37:51 wiz Exp $
-#
+# $NetBSD: Makefile,v 1.5 2017/12/17 14:30:36 bacon Exp $
-DISTNAME= bwa-0.7.9a
+DISTNAME= bwa-0.7.17
CATEGORIES= biology
-MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=bio-bwa/}
-EXTRACT_SUFX= .tar.bz2
-PKGREVISION= 2
+GITHUB_TAG= v${PKGVERSION_NOREV}
+MASTER_SITES= ${MASTER_SITE_GITHUB:=lh3/}
-MAINTAINER= jwbacon%tds.net@localhost
+MAINTAINER= bacon%NetBSD.org@localhost
HOMEPAGE= http://bio-bwa.sourceforge.net/
COMMENT= Map low-divergent sequences against a large reference genome
LICENSE= gnu-gpl-v3
Index: pkgsrc/biology/bwa/distinfo
diff -u pkgsrc/biology/bwa/distinfo:1.4 pkgsrc/biology/bwa/distinfo:1.5
--- pkgsrc/biology/bwa/distinfo:1.4 Tue Feb 14 21:34:34 2017
+++ pkgsrc/biology/bwa/distinfo Sun Dec 17 14:30:36 2017
@@ -1,8 +1,7 @@
-$NetBSD: distinfo,v 1.4 2017/02/14 21:34:34 joerg Exp $
+$NetBSD: distinfo,v 1.5 2017/12/17 14:30:36 bacon Exp $
-SHA1 (bwa-0.7.9a.tar.bz2) = a77ce327e8acba554b1d27bfdd1c148f79726484
-RMD160 (bwa-0.7.9a.tar.bz2) = a51b7c686a206144eab2aee0a372d5ae46fcfce1
-SHA512 (bwa-0.7.9a.tar.bz2) = 93804b2c0ac0f675e76f762441e1eec039d7f1cf77b033fd88f2e6c39d9cd4b5c21bba9fb44e34a3dab28c630c3855792a707e5b33109d4be0097cec97eaa686
-Size (bwa-0.7.9a.tar.bz2) = 166193 bytes
-SHA1 (patch-Makefile) = 2bb665cb579d20a07ae7c2be8ba0ed874d60d5b0
-SHA1 (patch-kopen.c) = 9c92b812a7e55bf9d7d136d91be02982610d9f51
+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) = 72ac08d92540a88da08bf4d988ca3f6132327a6a
Index: pkgsrc/biology/bwa/patches/patch-Makefile
diff -u pkgsrc/biology/bwa/patches/patch-Makefile:1.1 pkgsrc/biology/bwa/patches/patch-Makefile:1.2
--- pkgsrc/biology/bwa/patches/patch-Makefile:1.1 Sat Dec 12 16:56:04 2015
+++ pkgsrc/biology/bwa/patches/patch-Makefile Sun Dec 17 14:30:36 2017
@@ -1,24 +1,44 @@
-$NetBSD: patch-Makefile,v 1.1 2015/12/12 16:56:04 wiedi Exp $
+$NetBSD: patch-Makefile,v 1.2 2017/12/17 14:30:36 bacon Exp $
-Don't overwrite pkgsrc CC and CFLAGS
-
---- Makefile.orig 2014-05-19 13:11:41.000000000 +0000
+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?= gcc
#CC= clang --analyze
-CFLAGS= -g -Wall -Wno-unused-function -O2
-+#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)
-@@ -11,7 +11,7 @@ AOBJS= QSufSort.o bwt_gen.o bwase.o bwa
+@@ -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
-+LIBS= -lm -lz -lpthread $(LDFLAGS)
++LDFLAGS+= -lm -lz -lpthread
SUBDIRS= .
+ ifeq ($(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)
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