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- Fix installing scripts and support binaries

Browse Source 
- Add LICENSE

PR:		223098
Submitted by:	mzaki@niid.go.jp
This commit is contained in:
Wen Heping 2017-10-30 02:27:23 +00:00
parent d91015f8f4
commit eaf75bad8d
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=453152
4 changed files with 39 additions and 8 deletions
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26
biology/mummer/Makefile
View File

@ -3,7 +3,7 @@
PORTNAME= mummer
PORTVERSION= 3.23
PORTREVISION= 1
PORTREVISION= 2
CATEGORIES= biology
MASTER_SITES= SF
DISTNAME= MUMmer${PORTVERSION}
@ -11,20 +11,36 @@ DISTNAME= MUMmer${PORTVERSION}
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
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}

1
biology/mummer/distinfo
View File

@ -1,2 +1,3 @@
TIMESTAMP = 1509357521
SHA256 (MUMmer3.23.tar.gz) = 1efad4f7d8cee0d8eaebb320a2d63745bb3a160bb513a15ef7af46f330af662f
SIZE (MUMmer3.23.tar.gz) = 3160143

14
biology/mummer/files/patch-Makefile
View File

@ -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:

6
biology/mummer/pkg-plist
View File

@ -19,6 +19,12 @@ bin/show-coords
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