diff options
| author | bacon <bacon@pkgsrc.org> | 2017-12-17 14:30:36 +0000 |
|---|---|---|
| committer | bacon <bacon@pkgsrc.org> | 2017-12-17 14:30:36 +0000 |
| commit | 59fd6da94889076204aec033fd3c13f1685c6986 (patch) | |
| tree | a5c9a5e8a4fc70b3ff6480e6bcb0330e4489367d /biology | |
| parent | 013636da4cdb5af8bd4eff5238e418b46128c739 (diff) | |
| download | pkgsrc-59fd6da94889076204aec033fd3c13f1685c6986.tar.gz | |
biology/bwa: Update to 0.7.17
Numerous bug fixes, enhancements, and new command-line options
ok wiz@
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/bwa/Makefile | 12 | ||||
| -rw-r--r-- | biology/bwa/distinfo | 13 | ||||
| -rw-r--r-- | biology/bwa/patches/patch-Makefile | 36 | ||||
| -rw-r--r-- | biology/bwa/patches/patch-kopen.c | 12 |
4 files changed, 39 insertions, 34 deletions
diff --git a/biology/bwa/Makefile b/biology/bwa/Makefile index 4f122338d9c..05a6870f52b 100644 --- a/biology/bwa/Makefile +++ b/biology/bwa/Makefile @@ -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= ${MASTER_SITE_GITHUB:=lh3/} -MAINTAINER= jwbacon@tds.net +MAINTAINER= bacon@NetBSD.org HOMEPAGE= http://bio-bwa.sourceforge.net/ COMMENT= Map low-divergent sequences against a large reference genome LICENSE= gnu-gpl-v3 diff --git a/biology/bwa/distinfo b/biology/bwa/distinfo index 272019d4474..abf8b8cd593 100644 --- a/biology/bwa/distinfo +++ b/biology/bwa/distinfo @@ -1,8 +1,7 @@ -$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 diff --git a/biology/bwa/patches/patch-Makefile b/biology/bwa/patches/patch-Makefile index beec4b03f6e..280d2cfa63b 100644 --- a/biology/bwa/patches/patch-Makefile +++ b/biology/bwa/patches/patch-Makefile @@ -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 $@ $(LOBJS) diff --git a/biology/bwa/patches/patch-kopen.c b/biology/bwa/patches/patch-kopen.c deleted file mode 100644 index a1b28b37620..00000000000 --- a/biology/bwa/patches/patch-kopen.c +++ /dev/null @@ -1,12 +0,0 @@ -$NetBSD: patch-kopen.c,v 1.1 2017/02/14 21:34:34 joerg Exp $ - ---- kopen.c.orig 2017-02-09 15:42:47.246248867 +0000 -+++ kopen.c -@@ -8,6 +8,7 @@ - #include <signal.h> - #include <sys/wait.h> - #include <sys/types.h> -+#include <sys/time.h> - #ifndef _WIN32 - #include <netdb.h> - #include <arpa/inet.h> |