diff options
-rw-r--r-- | biology/mummer/Makefile | 8 | ||||
-rw-r--r-- | biology/mummer/PLIST | 4 | ||||
-rw-r--r-- | biology/mummer/distinfo | 11 | ||||
-rw-r--r-- | biology/mummer/patches/patch-aa | 24 | ||||
-rw-r--r-- | biology/mummer/patches/patch-ad | 23 |
5 files changed, 25 insertions, 45 deletions
diff --git a/biology/mummer/Makefile b/biology/mummer/Makefile index e8ee176200e..04190ef8564 100644 --- a/biology/mummer/Makefile +++ b/biology/mummer/Makefile @@ -1,8 +1,8 @@ -# $NetBSD: Makefile,v 1.17 2008/05/25 21:42:20 joerg Exp $ +# $NetBSD: Makefile,v 1.18 2008/10/11 22:01:13 schwarz Exp $ # -DISTNAME= MUMmer3.19 -PKGNAME= mummer-3.19 +DISTNAME= MUMmer3.20 +PKGNAME= mummer-3.20 CATEGORIES= biology MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=mummer/} @@ -30,7 +30,7 @@ do-install: ${INSTALL_PROGRAM} ${WRKSRC}/aux_bin/${p} ${DESTDIR}${PREFIX}/bin .endfor .for f in run-mummer1 run-mummer3 nucmer promer exact-tandems \ - mapview mummerplot nucmer2xfig + mapview mummerplot nucmer2xfig dnadiff ${INSTALL_SCRIPT} ${WRKSRC}/${f} ${DESTDIR}${PREFIX}/share/mummer .endfor cd ${WRKSRC}/docs && pax -wr -s ',^Makefile$$,,' * \ diff --git a/biology/mummer/PLIST b/biology/mummer/PLIST index 32948e95ba5..7c07fdc68f4 100644 --- a/biology/mummer/PLIST +++ b/biology/mummer/PLIST @@ -1,4 +1,4 @@ -@comment $NetBSD: PLIST,v 1.5 2007/01/18 19:13:10 rillig Exp $ +@comment $NetBSD: PLIST,v 1.6 2008/10/11 22:01:13 schwarz Exp $ bin/annotate bin/combineMUMs bin/delta-filter @@ -16,6 +16,7 @@ bin/show-snps bin/show-tiling share/doc/mummer/README share/doc/mummer/differences.README +share/doc/mummer/dnadiff.README share/doc/mummer/mapview.README share/doc/mummer/maxmat3man.tex share/doc/mummer/maxmat3src.pdf @@ -91,6 +92,7 @@ share/doc/mummer/web/manual/osi.gif share/doc/mummer/web/manual/pro_proex.gif share/doc/mummer/web/mummer-help.gif share/doc/mummer/web/mummer-users.gif +share/mummer/dnadiff share/mummer/exact-tandems share/mummer/mapview share/mummer/mummerplot diff --git a/biology/mummer/distinfo b/biology/mummer/distinfo index 45af2ccb057..f8ba432be0f 100644 --- a/biology/mummer/distinfo +++ b/biology/mummer/distinfo @@ -1,9 +1,8 @@ -$NetBSD: distinfo,v 1.8 2007/01/18 19:13:10 rillig Exp $ +$NetBSD: distinfo,v 1.9 2008/10/11 22:01:13 schwarz Exp $ -SHA1 (MUMmer3.19.tar.gz) = 8906bab6bd43b307461de8b5f44122a115799533 -RMD160 (MUMmer3.19.tar.gz) = 54f3c692efb8bde7762c48186919754f2a8c178c -Size (MUMmer3.19.tar.gz) = 3141991 bytes -SHA1 (patch-aa) = e40b6538b259475def39cd8008af37d0a08e1555 +SHA1 (MUMmer3.20.tar.gz) = 68d6742de93d8524236ccf538f32ba8bb4edf7cc +RMD160 (MUMmer3.20.tar.gz) = 7e5fefef359c6a6ee49f2ebf14dc18caa19f48fb +Size (MUMmer3.20.tar.gz) = 3155446 bytes +SHA1 (patch-aa) = 0f719a55e3c4f2994060f2b3f3ab4eb83519376f SHA1 (patch-ab) = af42da79fd287786cb83efa9c9b4fc8025abd728 SHA1 (patch-ac) = 7f0f16bdd83bc80833f1ffdcfe1bad7c2ee76eec -SHA1 (patch-ad) = 0804b2c966d7035c23444c4f72e1d93e45805bcf diff --git a/biology/mummer/patches/patch-aa b/biology/mummer/patches/patch-aa index 4f3836d2822..3e712e74e61 100644 --- a/biology/mummer/patches/patch-aa +++ b/biology/mummer/patches/patch-aa @@ -1,35 +1,37 @@ -$NetBSD: patch-aa,v 1.5 2007/01/18 19:13:10 rillig Exp $ +$NetBSD: patch-aa,v 1.6 2008/10/11 22:01:13 schwarz Exp $ ---- Makefile.orig 2003-07-09 09:49:51.000000000 -0400 -+++ Makefile 2003-09-27 18:15:34.000000000 -0400 +--- Makefile.orig 2008-10-05 16:48:07.000000000 +0200 ++++ Makefile 2008-10-05 16:49:50.000000000 +0200 @@ -22,7 +22,7 @@ # 'make uninstall' alias for 'make clean' (for compatibility) # #------------------------------------------------------------------------------- -SHELL = /bin/sh +SHELL = ${SH} - VERSION := 3.19 + VERSION := 3.20 -@@ -35,15 +35,12 @@ +@@ -35,15 +35,15 @@ TIGR_SRC_DIR := $(TOP_DIR)/src/tigr KURTZ_SRC_DIR := $(TOP_DIR)/src/kurtz -CC := $(filter /%,$(shell /bin/sh -c 'type gcc')) -CXX := $(filter /%,$(shell /bin/sh -c 'type g++')) -SED := $(filter /%,$(shell /bin/sh -c 'type sed')) +-CSH := $(filter /%,$(shell /bin/sh -c 'type csh')) +-PERL := $(filter /%,$(shell /bin/sh -c 'type perl')) +-AR := $(filter /%,$(shell /bin/sh -c 'type ar')) +#CC := $(filter /%,$(shell /bin/sh -c 'type gcc')) +#CXX := $(filter /%,$(shell /bin/sh -c 'type g++')) +#SED := $(filter /%,$(shell /bin/sh -c 'type sed')) --CSH := $(filter /%,$(shell /bin/sh -c 'type csh')) +#CSH := $(filter /%,$(shell /bin/sh -c 'type csh')) --PERL := $(filter /%,$(shell /bin/sh -c 'type perl')) --AR := $(filter /%,$(shell /bin/sh -c 'type ar')) -- --CPPFLAGS = -Wall -O3 --LDFLAGS = +#PERL := $(filter /%,$(shell /bin/sh -c 'type perl')) +#AR := $(filter /%,$(shell /bin/sh -c 'type ar')) +-CPPFLAGS = -Wall -O3 +-LDFLAGS = ++#CPPFLAGS = -Wall -O3 ++#LDFLAGS = + FLATS = ACKNOWLEDGEMENTS COPYRIGHT INSTALL LICENSE Makefile README ChangeLog diff --git a/biology/mummer/patches/patch-ad b/biology/mummer/patches/patch-ad deleted file mode 100644 index 6056f94ed86..00000000000 --- a/biology/mummer/patches/patch-ad +++ /dev/null @@ -1,23 +0,0 @@ -$NetBSD: patch-ad,v 1.1 2006/04/19 16:50:36 joerg Exp $ - ---- src/kurtz/mm3src/Makefile.orig 2006-04-19 16:36:40.000000000 +0000 -+++ src/kurtz/mm3src/Makefile -@@ -40,15 +40,15 @@ SPLINTALL=maxmat3.splint maxmatopt.splin - all: $(ALL) - - mummer: $(MUM3OBJECTS) $(LIBSTREE) -- $(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE)\ -+ $(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \ - -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@ - - maxmat3.x: $(MUM3OBJECTS) $(LIBSTREE) -- $(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE)\ -+ $(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \ - -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@ - - maxmat3.dbg.x: ${MUM3DBGOBJECTS} $(LIBSTREEDBG) -- $(LD) $(LDFLAGS) $(MUM3DBGOBJECTS) $(LIBSTREEDBG) $(LIBBASEDBG)\ -+ $(LD) $(LDFLAGS) $(MUM3DBGOBJECTS) $(LIBSTREEDBG) $(LIBBASEDBG) \ - -lm -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@ - - include Filegoals.mf |