From owner-svn-ports-all@freebsd.org Mon Oct 30 02:27:24 2017 Return-Path: Delivered-To: svn-ports-all@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id BB2BFE52081; Mon, 30 Oct 2017 02:27:24 +0000 (UTC) (envelope-from wen@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id 9571E6F7D7; Mon, 30 Oct 2017 02:27:24 +0000 (UTC) (envelope-from wen@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id v9U2RN3l099601; Mon, 30 Oct 2017 02:27:23 GMT (envelope-from wen@FreeBSD.org) Received: (from wen@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id v9U2RNvP099596; Mon, 30 Oct 2017 02:27:23 GMT (envelope-from wen@FreeBSD.org) Message-Id: <201710300227.v9U2RNvP099596@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: wen set sender to wen@FreeBSD.org using -f From: Wen Heping Date: Mon, 30 Oct 2017 02:27:23 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r453152 - in head/biology/mummer: . files X-SVN-Group: ports-head X-SVN-Commit-Author: wen X-SVN-Commit-Paths: in head/biology/mummer: . files X-SVN-Commit-Revision: 453152 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.23 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 30 Oct 2017 02:27:24 -0000 Author: wen Date: Mon Oct 30 02:27:23 2017 New Revision: 453152 URL: https://svnweb.freebsd.org/changeset/ports/453152 Log: - Fix installing scripts and support binaries - Add LICENSE PR: 223098 Submitted by: mzaki@niid.go.jp Modified: head/biology/mummer/Makefile head/biology/mummer/distinfo head/biology/mummer/files/patch-Makefile head/biology/mummer/pkg-plist Modified: head/biology/mummer/Makefile ============================================================================== --- head/biology/mummer/Makefile Mon Oct 30 01:43:55 2017 (r453151) +++ head/biology/mummer/Makefile Mon Oct 30 02:27:23 2017 (r453152) @@ -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} Modified: head/biology/mummer/distinfo ============================================================================== --- head/biology/mummer/distinfo Mon Oct 30 01:43:55 2017 (r453151) +++ head/biology/mummer/distinfo Mon Oct 30 02:27:23 2017 (r453152) @@ -1,2 +1,3 @@ +TIMESTAMP = 1509357521 SHA256 (MUMmer3.23.tar.gz) = 1efad4f7d8cee0d8eaebb320a2d63745bb3a160bb513a15ef7af46f330af662f SIZE (MUMmer3.23.tar.gz) = 3160143 Modified: head/biology/mummer/files/patch-Makefile ============================================================================== --- head/biology/mummer/files/patch-Makefile Mon Oct 30 01:43:55 2017 (r453151) +++ head/biology/mummer/files/patch-Makefile Mon Oct 30 02:27:23 2017 (r453152) @@ -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: Modified: head/biology/mummer/pkg-plist ============================================================================== --- head/biology/mummer/pkg-plist Mon Oct 30 01:43:55 2017 (r453151) +++ head/biology/mummer/pkg-plist Mon Oct 30 02:27:23 2017 (r453152) @@ -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