Attachment #187287 for bug #223098

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PORTNAME=	mummer
PORTVERSION=	3.23
PORTREVISION=	2
CATEGORIES=	biology
MASTER_SITES=	SF
DISTNAME=	MUMmer${PORTVERSION}

MAINTAINER=	ports@FreeBSD.org
COMMENT=	Modular system for rapid whole genome alignment

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.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


do-install:
	${INSTALL_PROGRAM} ${PROGRAMS:S|^|${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}





--- 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

-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
 AR   := $(filter /%,$(shell /bin/sh -c 'type ar'))
 
-CXXFLAGS = -O3

 
 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:

Lines 19-24 Link Here

(-)pkg-plist (+6 lines)
19	bin/show-diff	19	bin/show-diff
20	bin/show-snps	20	bin/show-snps
21	bin/show-tiling	21	bin/show-tiling
		22	libexec/mummer/Foundation.pm
		23	libexec/mummer/postnuc
		24	libexec/mummer/postpro
		25	libexec/mummer/prenuc
		26	libexec/mummer/prepro
		27	libexec/mummer/tandem-repeat.awk
22	%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT	28	%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
23	%%PORTDOCS%%%%DOCSDIR%%/INSTALL	29	%%PORTDOCS%%%%DOCSDIR%%/INSTALL
24	%%PORTDOCS%%%%DOCSDIR%%/LICENSE	30	%%PORTDOCS%%%%DOCSDIR%%/LICENSE

Return to bug 223098

Lines 3-9 Link Here

(-)Makefile (-5 / +21 lines)
3		3
4	PORTNAME= mummer	4	PORTNAME= mummer
5	PORTVERSION= 3.23	5	PORTVERSION= 3.23
6	PORTREVISION= 1	6	PORTREVISION= 2
7	CATEGORIES= biology	7	CATEGORIES= biology
8	MASTER_SITES= SF	8	MASTER_SITES= SF
9	DISTNAME= MUMmer${PORTVERSION}	9	DISTNAME= MUMmer${PORTVERSION}
Lines 11-23 Link Here
11	MAINTAINER= ports@FreeBSD.org	11	MAINTAINER= ports@FreeBSD.org
12	COMMENT= Modular system for rapid whole genome alignment	12	COMMENT= Modular system for rapid whole genome alignment
13		13
14	USES= gmake perl5	14	LICENSE= ART10
		15	LICENSE_FILE= ${WRKSRC}/LICENSE
15		16
		17	USES= gmake perl5 shebangfix
		18
		19	SHEBANG_FILES= scripts/.csh scripts/.pl
		20	SHEBANG_LANG= csh
		21	perl_OLD_CMD= __PERL_PATH
		22	csh_OLD_CMD= __CSH_PATH
		23	csh_CMD= /bin/csh
		24	_SHEBANG_REINPLACE_ARGS+= -e "s\|__BIN_DIR\|${PREFIX}/bin\|g;s\|__AUX_BIN_DIR\|${PREFIX}/libexec/mummer\|g;s\|__SCRIPT_DIR\|${PREFIX}/libexec/mummer\|g"
		25
16	PROGRAMS= annotate combineMUMs delta-filter gaps \	26	PROGRAMS= annotate combineMUMs delta-filter gaps \
17	mgaps mummer repeat-match show-aligns \	27	mgaps mummer repeat-match show-aligns \
18	show-coords show-diff show-snps show-tiling	28	show-coords show-diff show-snps show-tiling
19	SCRIPTS= dnadiff exact-tandems mapview mummerplot nucmer \	29	SCRIPTS= dnadiff.pl exact-tandems.csh mapview.pl mummerplot.pl nucmer.pl \
20	nucmer2xfig promer run-mummer1 run-mummer3	30	nucmer2xfig.pl promer.pl run-mummer1.csh run-mummer3.csh
		31	LIBEXEC= Foundation.pm tandem-repeat.awk
21	DOCUMENTS= COPYRIGHT INSTALL LICENSE README	32	DOCUMENTS= COPYRIGHT INSTALL LICENSE README
22		33
23	OPTIONS_DEFINE= DOCS	34	OPTIONS_DEFINE= DOCS
Lines 24-30 Link Here
24		35
25	do-install:	36	do-install:
26	${INSTALL_PROGRAM} ${PROGRAMS:S\|^\|${WRKSRC}/\|} ${STAGEDIR}${PREFIX}/bin	37	${INSTALL_PROGRAM} ${PROGRAMS:S\|^\|${WRKSRC}/\|} ${STAGEDIR}${PREFIX}/bin
27	${INSTALL_SCRIPT} ${SCRIPTS:S\|^\|${WRKSRC}/\|} ${STAGEDIR}${PREFIX}/bin	38	.for file in ${SCRIPTS}
		39	${INSTALL_SCRIPT} ${WRKSRC}/scripts/${file} ${STAGEDIR}${PREFIX}/bin/${file:R}
		40	.endfor
		41	@${MKDIR} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME}
		42	${INSTALL_PROGRAM} ${WRKSRC}/aux_bin/* ${STAGEDIR}${PREFIX}/libexec/${PORTNAME}
		43	${INSTALL_DATA} ${LIBEXEC:S\|^\|${WRKSRC}/scripts/\|} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME}
28	@${MKDIR} ${STAGEDIR}${DOCSDIR}	44	@${MKDIR} ${STAGEDIR}${DOCSDIR}
29	${INSTALL_DATA} ${DOCUMENTS:S\|^\|${WRKSRC}/\|} ${STAGEDIR}${DOCSDIR}	45	${INSTALL_DATA} ${DOCUMENTS:S\|^\|${WRKSRC}/\|} ${STAGEDIR}${DOCSDIR}
30		46

Lines 1-4 Link Here

(-)files/patch-Makefile (-3 / +11 lines)
1	--- Makefile.orig 2015-08-05 01:03:53 UTC	1	--- Makefile.orig 2011-12-17 02:49:27 UTC
2	+++ Makefile	2	+++ Makefile
3	@@ -35,16 +35,11 @@ SCRIPT_DIR := $(TOP_DIR)/scripts	3	@@ -35,16 +35,11 @@ SCRIPT_DIR := $(TOP_DIR)/scripts
4	TIGR_SRC_DIR := $(TOP_DIR)/src/tigr	4	TIGR_SRC_DIR := $(TOP_DIR)/src/tigr
Lines 8-15 Link Here
8	-CXX := $(filter /%,$(shell /bin/sh -c 'type g++'))	8	-CXX := $(filter /%,$(shell /bin/sh -c 'type g++'))
9	SED := $(filter /%,$(shell /bin/sh -c 'type sed'))	9	SED := $(filter /%,$(shell /bin/sh -c 'type sed'))
10	CSH := $(filter /%,$(shell /bin/sh -c 'type csh'))	10	CSH := $(filter /%,$(shell /bin/sh -c 'type csh'))
11	-PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))	11	PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))
12	+PERL := ${LOCALBASE}/bin/perl
13	AR := $(filter /%,$(shell /bin/sh -c 'type ar'))	12	AR := $(filter /%,$(shell /bin/sh -c 'type ar'))
14		13
15	-CXXFLAGS = -O3	14	-CXXFLAGS = -O3
Lines 18-20 Link Here
18		17
19	FLATS = ACKNOWLEDGEMENTS COPYRIGHT INSTALL LICENSE Makefile README ChangeLog	18	FLATS = ACKNOWLEDGEMENTS COPYRIGHT INSTALL LICENSE Makefile README ChangeLog
20		19
		20	@@ -60,7 +55,7 @@ export BIN_DIR AUX_BIN_DIR CXX CC CFLAGS
		21	.PHONY: all check clean dist scripts uninstall
		22
		23
		24	-all: kurtz tigr scripts
		25	+all: kurtz tigr
		26
		27
		28	check: