From owner-svn-ports-head@FreeBSD.ORG Tue May 20 19:35:31 2014 Return-Path: Delivered-To: svn-ports-head@freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id 7C0F49E7; Tue, 20 May 2014 19:35:31 +0000 (UTC) Received: from svn.freebsd.org (svn.freebsd.org [IPv6:2001:1900:2254:2068::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 683D82933; Tue, 20 May 2014 19:35:31 +0000 (UTC) Received: from svn.freebsd.org ([127.0.1.70]) by svn.freebsd.org (8.14.8/8.14.8) with ESMTP id s4KJZVMk048276; Tue, 20 May 2014 19:35:31 GMT (envelope-from amdmi3@svn.freebsd.org) Received: (from amdmi3@localhost) by svn.freebsd.org (8.14.8/8.14.8/Submit) id s4KJZUxt048273; Tue, 20 May 2014 19:35:30 GMT (envelope-from amdmi3@svn.freebsd.org) Message-Id: <201405201935.s4KJZUxt048273@svn.freebsd.org> From: Dmitry Marakasov Date: Tue, 20 May 2014 19:35:30 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r354673 - head/biology/mafft X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 20 May 2014 19:35:31 -0000 Author: amdmi3 Date: Tue May 20 19:35:30 2014 New Revision: 354673 URL: http://svnweb.freebsd.org/changeset/ports/354673 QAT: https://qat.redports.org/buildarchive/r354673/ Log: - Update to 7.149 - Clarify LICENSE - Stagify PR: 189746 Submitted by: "Reed A. Cartwright" (maintainer) Modified: head/biology/mafft/Makefile head/biology/mafft/distinfo head/biology/mafft/pkg-plist Modified: head/biology/mafft/Makefile ============================================================================== --- head/biology/mafft/Makefile Tue May 20 19:35:29 2014 (r354672) +++ head/biology/mafft/Makefile Tue May 20 19:35:30 2014 (r354673) @@ -1,8 +1,8 @@ -# Created by: Fernan Aguero +# Created by: Reed A. Cartwright # $FreeBSD$ PORTNAME= mafft -PORTVERSION= 6.903 +PORTVERSION= 7.149 CATEGORIES= biology MASTER_SITES= http://mafft.cbrc.jp/alignment/software/ DISTNAME= ${PORTNAME}-${PORTVERSION}-without-extensions-src @@ -11,28 +11,27 @@ EXTRACT_SUFX= .tgz MAINTAINER= cartwright@asu.edu COMMENT= Multiple alignment program for amino acid or nucleotide sequences -LICENSE= BSD - -RUN_DEPENDS= lav2ps:${PORTSDIR}/biology/fasta3 +LICENSE= BSD2CLAUSE WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}-without-extensions BUILD_WRKSRC= ${WRKSRC}/core -USES= gmake +USES= gmake shebangfix -MAN1= mafft.1 mafft-homologs.1 +SHEBANG_FILES= core/mafftash_premafft.tmpl LIBEXEC_FILES= dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \ - pair2hat3s multi2hat3s rnatest pairash addsingle splittbfast \ + pair2hat3s multi2hat3s pairash addsingle splittbfast \ disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap \ - countlen seq2regtable regtable2seq score getlag dndpre dndpre2 \ + countlen seq2regtable regtable2seq score getlag dndpre \ setcore replaceu restoreu setdirection makedirectionlist version +PERL_LIBEXEC_FILES= mafftash_premafft.pl SCRIPT_FILES= mafft mafft-homologs.rb LN_FILES= einsi fftns fftnsi ginsi linsi mafft-einsi mafft-fftns \ mafft-fftnsi mafft-ginsi mafft-linsi mafft-nwns mafft-nwnsi \ mafft-qinsi mafft-xinsi nwns nwnsi +MAN1_FILES= mafft.1 mafft-homologs.1 -NO_STAGE= yes .include .if ${ARCH} == "sparc64" @@ -48,27 +47,28 @@ post-patch: ${BUILD_WRKSRC}/Makefile do-install: - @${MKDIR} ${PREFIX}/libexec/${PORTNAME} + @${MKDIR} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME} .for exec in ${LIBEXEC_FILES} - ${INSTALL_PROGRAM} ${WRKSRC}/binaries/${exec} ${PREFIX}/libexec/${PORTNAME} + ${INSTALL_PROGRAM} ${WRKSRC}/binaries/${exec} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME} +.endfor +.for exec in ${PERL_LIBEXEC_FILES} + ${INSTALL_SCRIPT} ${WRKSRC}/binaries/${exec} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME} .endfor .for exec in ${SCRIPT_FILES} - ${INSTALL_SCRIPT} ${WRKSRC}/scripts/${exec} ${PREFIX}/bin + ${INSTALL_SCRIPT} ${WRKSRC}/scripts/${exec} ${STAGEDIR}${PREFIX}/bin .endfor .for exec in ${LN_FILES} - ${LN} -fs ${PREFIX}/bin/mafft ${PREFIX}/bin/${exec} + ${LN} -sf mafft ${STAGEDIR}${PREFIX}/bin/${exec} .endfor - ${LN} -fs ${PREFIX}/libexec/${PORTNAME}/mafft-distance ${PREFIX}/bin/mafft-distance - ${LN} -fs ${PREFIX}/libexec/${PORTNAME}/mafft-profile ${PREFIX}/bin/mafft-profile -.for man in ${MAN1} - ${INSTALL_MAN} ${WRKSRC}/binaries/${man} ${MAN1PREFIX}/man/man1 + ${LN} -sf ../libexec/${PORTNAME}/mafft-distance ${STAGEDIR}${PREFIX}/bin/mafft-distance + ${LN} -sf ../libexec/${PORTNAME}/mafft-profile ${STAGEDIR}${PREFIX}/bin/mafft-profile +.for man in ${MAN1_FILES} + ${INSTALL_MAN} ${WRKSRC}/binaries/${man} ${STAGEDIR}${MAN1PREFIX}/man/man1 .endfor - @${MKDIR} ${EXAMPLESDIR} - ${INSTALL_DATA} ${WRKSRC}/test/* ${EXAMPLESDIR} -.if ${PORT_OPTIONS:MDOCS} - @${MKDIR} ${DOCSDIR} - ${INSTALL_DATA} ${WRKSRC}/readme ${DOCSDIR} - ${INSTALL_DATA} ${WRKSRC}/license ${DOCSDIR} -.endif + @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} + ${INSTALL_DATA} ${WRKSRC}/test/* ${STAGEDIR}${EXAMPLESDIR} + @${MKDIR} ${STAGEDIR}${DOCSDIR} + ${INSTALL_DATA} ${WRKSRC}/readme ${STAGEDIR}${DOCSDIR} + ${INSTALL_DATA} ${WRKSRC}/license ${STAGEDIR}${DOCSDIR} .include Modified: head/biology/mafft/distinfo ============================================================================== --- head/biology/mafft/distinfo Tue May 20 19:35:29 2014 (r354672) +++ head/biology/mafft/distinfo Tue May 20 19:35:30 2014 (r354673) @@ -1,2 +1,2 @@ -SHA256 (mafft-6.903-without-extensions-src.tgz) = d96326aecdb1f86b63779312c4a6d8f719f32786396567c1d1829341fc6dbcc8 -SIZE (mafft-6.903-without-extensions-src.tgz) = 359536 +SHA256 (mafft-7.149-without-extensions-src.tgz) = cfd909ee28afcc191f99c7ca37a507ddbefe9fbc416ef5692528c68a60c7b29a +SIZE (mafft-7.149-without-extensions-src.tgz) = 373846 Modified: head/biology/mafft/pkg-plist ============================================================================== --- head/biology/mafft/pkg-plist Tue May 20 19:35:29 2014 (r354672) +++ head/biology/mafft/pkg-plist Tue May 20 19:35:30 2014 (r354673) @@ -25,12 +25,12 @@ libexec/mafft/disttbfast libexec/mafft/dndblast libexec/mafft/dndfast7 libexec/mafft/dndpre -libexec/mafft/dndpre2 libexec/mafft/dvtditr libexec/mafft/f2cl libexec/mafft/getlag libexec/mafft/mafft-distance libexec/mafft/mafft-profile +libexec/mafft/mafftash_premafft.pl libexec/mafft/makedirectionlist libexec/mafft/mccaskillwrap libexec/mafft/multi2hat3s @@ -40,7 +40,6 @@ libexec/mafft/pairlocalalign libexec/mafft/regtable2seq libexec/mafft/replaceu libexec/mafft/restoreu -libexec/mafft/rnatest libexec/mafft/score libexec/mafft/seq2regtable libexec/mafft/setcore @@ -49,20 +48,24 @@ libexec/mafft/sextet5 libexec/mafft/splittbfast libexec/mafft/tbfast libexec/mafft/version +man/man1/mafft-homologs.1.gz +man/man1/mafft.1.gz %%PORTDOCS%%%%DOCSDIR%%/license %%PORTDOCS%%%%DOCSDIR%%/readme %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.allowshift %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.dpparttree %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.fftns2 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.fftnsi %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.gins1 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.ginsi +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.ginsi.allowshift %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.lins1 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.linsi %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.parttree %%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna %%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna.qinsi %%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna.xinsi -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%% -%%PORTDOCS%%@dirrm %%DOCSDIR%% -@dirrm libexec/mafft +@dirrmtry libexec/mafft +%%PORTDOCS%%@dirrmtry %%DOCSDIR%% +%%PORTEXAMPLES%%@dirrmtry %%EXAMPLESDIR%%