Date: Mon, 12 May 2014 19:14:02 -0700 (MST) From: "Reed A. Cartwright" <cartwright@asu.edu> To: FreeBSD-gnats-submit@freebsd.org Subject: ports/189746: [maintainer update] Update biology/mafft Message-ID: <201405130214.s4D2E2vS094301@herschel.biodesign.asu.edu> Resent-Message-ID: <201405130240.s4D2e0XP051734@freefall.freebsd.org>
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>Number: 189746 >Category: ports >Synopsis: [maintainer update] Update biology/mafft >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: maintainer-update >Submitter-Id: current-users >Arrival-Date: Tue May 13 02:40:00 UTC 2014 >Closed-Date: >Last-Modified: >Originator: Reed A. Cartwright >Release: FreeBSD 10.0-RELEASE-p2 amd64 >Organization: ASU >Environment: System: FreeBSD herschel.biodesign.asu.edu 10.0-RELEASE-p2 FreeBSD 10.0-RELEASE-p2 #0: Tue Apr 29 17:06:01 UTC 2014 root@amd64-builder.daemonology.net:/usr/obj/usr/src/sys/GENERIC amd64 >Description: Update biology/mafft to 7.149 and support staging >How-To-Repeat: >Fix: Patch is attached --- mafft.diff begins here --- Index: Makefile =================================================================== --- Makefile (revision 353911) +++ Makefile (working copy) @@ -1,8 +1,8 @@ -# Created by: Fernan Aguero <fernan@iib.unsam.edu.ar> +# Created by: Reed A. Cartwright <reed@cartwrig.ht> # $FreeBSD$ 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 @@ MAINTAINER= cartwright@asu.edu COMMENT= Multiple alignment program for amino acid or nucleotide sequences -LICENSE= BSD +LICENSE= BSD2CLAUSE -RUN_DEPENDS= lav2ps:${PORTSDIR}/biology/fasta3 - 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 <bsd.port.pre.mk> .if ${ARCH} == "sparc64" @@ -48,27 +47,28 @@ ${BUILD_WRKSRC}/Makefile do-install: - @${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 <bsd.port.post.mk> Index: distinfo =================================================================== --- distinfo (revision 353911) +++ distinfo (working copy) @@ -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 Index: pkg-plist =================================================================== --- pkg-plist (revision 353911) +++ pkg-plist (working copy) @@ -25,12 +25,12 @@ 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/regtable2seq libexec/mafft/replaceu libexec/mafft/restoreu -libexec/mafft/rnatest libexec/mafft/score libexec/mafft/seq2regtable libexec/mafft/setcore @@ -49,14 +48,18 @@ 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 @@ -63,6 +66,6 @@ %%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%% --- mafft.diff ends here --- >Release-Note: >Audit-Trail: >Unformatted:
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