Attachment 187287 Details for Bug 223098 – svn diff for biology/mummer

[patch] svn diff for biology/mummer

mummer-3.23_2.diff (text/plain), 3.37 KB, created by Motomichi Matsuzaki on 2017-10-18 17:27:31 UTC

(hide)

Description:

Filename:

MIME Type:

Creator: Motomichi Matsuzaki

Created: 2017-10-18 17:27:31 UTC

Size: 3.37 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 452355)
>+++ Makefile	(working copy)
>@@ -3,7 +3,7 @@
> 
> PORTNAME=	mummer
> PORTVERSION=	3.23
>-PORTREVISION=	1
>+PORTREVISION=	2
> CATEGORIES=	biology
> MASTER_SITES=	SF
> DISTNAME=	MUMmer${PORTVERSION}
>@@ -11,13 +11,24 @@
> MAINTAINER=	ports@FreeBSD.org
> COMMENT=	Modular system for rapid whole genome alignment
> 
>-USES=		gmake perl5
>+LICENSE=	ART10
>+LICENSE_FILE=	${WRKSRC}/LICENSE
> 
>+USES=		gmake perl5 shebangfix
>+
>+SHEBANG_FILES=	scripts/*.csh scripts/*.pl
>+SHEBANG_LANG=	csh
>+perl_OLD_CMD=	__PERL_PATH
>+csh_OLD_CMD=	__CSH_PATH
>+csh_CMD=	/bin/csh
>+_SHEBANG_REINPLACE_ARGS+=	-e "s|__BIN_DIR|${PREFIX}/bin|g;s|__AUX_BIN_DIR|${PREFIX}/libexec/mummer|g;s|__SCRIPT_DIR|${PREFIX}/libexec/mummer|g"
>+
> PROGRAMS=	annotate combineMUMs delta-filter gaps \
> 		mgaps mummer repeat-match show-aligns \
> 		show-coords show-diff show-snps show-tiling
>-SCRIPTS=	dnadiff exact-tandems mapview mummerplot nucmer \
>-		nucmer2xfig promer run-mummer1 run-mummer3
>+SCRIPTS=	dnadiff.pl exact-tandems.csh mapview.pl mummerplot.pl nucmer.pl \
>+		nucmer2xfig.pl promer.pl run-mummer1.csh run-mummer3.csh
>+LIBEXEC=	Foundation.pm tandem-repeat.awk
> DOCUMENTS=	COPYRIGHT INSTALL LICENSE README
> 
> OPTIONS_DEFINE=	DOCS
>@@ -24,7 +35,12 @@
> 
> do-install:
> 	${INSTALL_PROGRAM} ${PROGRAMS:S|^|${WRKSRC}/|} ${STAGEDIR}${PREFIX}/bin
>-	${INSTALL_SCRIPT} ${SCRIPTS:S|^|${WRKSRC}/|} ${STAGEDIR}${PREFIX}/bin
>+.for file in ${SCRIPTS}
>+	${INSTALL_SCRIPT} ${WRKSRC}/scripts/${file} ${STAGEDIR}${PREFIX}/bin/${file:R}
>+.endfor
>+	@${MKDIR} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME}
>+	${INSTALL_PROGRAM} ${WRKSRC}/aux_bin/* ${STAGEDIR}${PREFIX}/libexec/${PORTNAME}
>+	${INSTALL_DATA} ${LIBEXEC:S|^|${WRKSRC}/scripts/|} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME}
> 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
> 	${INSTALL_DATA} ${DOCUMENTS:S|^|${WRKSRC}/|} ${STAGEDIR}${DOCSDIR}
> 
>Index: files/patch-Makefile
>===================================================================
>--- files/patch-Makefile	(revision 452355)
>+++ files/patch-Makefile	(working copy)
>@@ -1,4 +1,4 @@
>---- Makefile.orig	2015-08-05 01:03:53 UTC
>+--- Makefile.orig	2011-12-17 02:49:27 UTC
> +++ Makefile
> @@ -35,16 +35,11 @@ SCRIPT_DIR    := $(TOP_DIR)/scripts
>  TIGR_SRC_DIR  := $(TOP_DIR)/src/tigr
>@@ -8,8 +8,7 @@
> -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'))
>-+PERL := ${LOCALBASE}/bin/perl
>+ PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))
>  AR   := $(filter /%,$(shell /bin/sh -c 'type ar'))
>  
> -CXXFLAGS = -O3
>@@ -18,3 +17,12 @@
>  
>  FLATS = ACKNOWLEDGEMENTS COPYRIGHT INSTALL LICENSE Makefile README ChangeLog
>  
>+@@ -60,7 +55,7 @@ export BIN_DIR AUX_BIN_DIR CXX CC CFLAGS
>+ .PHONY: all check clean dist scripts uninstall
>+ 
>+ 
>+-all: kurtz tigr scripts
>++all: kurtz tigr
>+ 
>+ 
>+ check:
>Index: pkg-plist
>===================================================================
>--- pkg-plist	(revision 452355)
>+++ pkg-plist	(working copy)
>@@ -19,6 +19,12 @@
> bin/show-diff
> bin/show-snps
> bin/show-tiling
>+libexec/mummer/Foundation.pm
>+libexec/mummer/postnuc
>+libexec/mummer/postpro
>+libexec/mummer/prenuc
>+libexec/mummer/prepro
>+libexec/mummer/tandem-repeat.awk
> %%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
> %%PORTDOCS%%%%DOCSDIR%%/INSTALL
> %%PORTDOCS%%%%DOCSDIR%%/LICENSE

Actions: View | Diff

Attachments on bug 223098: 187287