From 2c946497bac39cd7d65ea8cb75e9fdbdab54a271 Mon Sep 17 00:00:00 2001 From: Michael Scheidell Date: Tue, 7 Aug 2012 12:26:39 +0000 Subject: [PATCH] - Update to version 6.903 PR: ports/169920 Submitted by: "Reed A. Cartwright" Approved by: maintainer (timeout, 21 days) --- biology/mafft/Makefile | 62 +++++++++++++++++++++------- biology/mafft/distinfo | 4 +- biology/mafft/pkg-descr | 6 ++- biology/mafft/pkg-plist | 91 +++++++++++++++++++++++++++++------------ 4 files changed, 119 insertions(+), 44 deletions(-) diff --git a/biology/mafft/Makefile b/biology/mafft/Makefile index c98d03b6a2e1..21fe2ffd611c 100644 --- a/biology/mafft/Makefile +++ b/biology/mafft/Makefile @@ -7,34 +7,68 @@ # PORTNAME= mafft -PORTVERSION= 5.743 +PORTVERSION= 6.903 CATEGORIES= biology -MASTER_SITES= http://align.bmr.kyushu-u.ac.jp/mafft/software/ -DISTNAME= ${PORTNAME}-${PORTVERSION}-src +MASTER_SITES= http://mafft.cbrc.jp/alignment/software/ +DISTNAME= ${PORTNAME}-${PORTVERSION}-without-extensions-src EXTRACT_SUFX= .tgz MAINTAINER= fernan@iib.unsam.edu.ar -COMMENT= Multiple sequence alignments based on fast Fourier transform +COMMENT= Multiple alignment program for amino acid or nucleotide sequences + +LICENSE= BSD RUN_DEPENDS= lav2ps:${PORTSDIR}/biology/fasta3 -WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION} -BUILD_WRKSRC= ${WRKSRC}/src +WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}-without-extensions +BUILD_WRKSRC= ${WRKSRC}/core -MAKE_ENV+= CFLAG="${CFLAGS}" +USE_GMAKE= yes + +MAN1= mafft.1 mafft-homologs.1 + +LIBEXEC_FILES= dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \ + pair2hat3s multi2hat3s rnatest pairash addsingle splittbfast \ + disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap \ + countlen seq2regtable regtable2seq score getlag dndpre dndpre2 \ + setcore replaceu restoreu setdirection makedirectionlist version +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 + +.include post-patch: - @${REINPLACE_CMD} -E 's,^(CC|PREFIX) =,\1 ?=,' \ - ${WRKSRC}/src/Makefile + @${REINPLACE_CMD} -e 's|-lpthread|${PTHREAD_LIBS}|' \ + -e 's|^MANDIR = .*$$|MANDIR = $$(MANPREFIX)/man/man1|' \ + -e 's|^PREFIX = .*$$||' \ + -e 's|^CC = .*$$||' \ + -e 's|^CFLAGS = .*$$||' \ + ${BUILD_WRKSRC}/Makefile do-install: - ${INSTALL_SCRIPT} ${WRKSRC}/scripts/mafft ${PREFIX}/bin - ${INSTALL_PROGRAM} ${WRKSRC}/binaries/* ${PREFIX}/bin - @ ${MKDIR} ${EXAMPLESDIR} + @${MKDIR} ${PREFIX}/libexec/${PORTNAME} +.for exec in ${LIBEXEC_FILES} + ${INSTALL_PROGRAM} ${WRKSRC}/binaries/${exec} ${PREFIX}/libexec/${PORTNAME} +.endfor +.for exec in ${SCRIPT_FILES} + ${INSTALL_SCRIPT} ${WRKSRC}/scripts/${exec} ${PREFIX}/bin +.endfor +.for exec in ${LN_FILES} + ${LN} -fs ${PREFIX}/bin/mafft ${PREFIX}/bin/${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} ${MAN1PREFIX}/man/man1 +.endfor + @${MKDIR} ${EXAMPLESDIR} ${INSTALL_DATA} ${WRKSRC}/test/* ${EXAMPLESDIR} .if !defined(NOPORTDOCS) - @ ${MKDIR} ${DOCSDIR} + @${MKDIR} ${DOCSDIR} ${INSTALL_DATA} ${WRKSRC}/readme ${DOCSDIR} + ${INSTALL_DATA} ${WRKSRC}/license ${DOCSDIR} .endif -.include +.include diff --git a/biology/mafft/distinfo b/biology/mafft/distinfo index 0540132eb40a..b19598a0b49e 100644 --- a/biology/mafft/distinfo +++ b/biology/mafft/distinfo @@ -1,2 +1,2 @@ -SHA256 (mafft-5.743-src.tgz) = 7bf0d450fea1d44fafee27c29c74b3ae4247ad0075b41729d9dc935e2a88de66 -SIZE (mafft-5.743-src.tgz) = 280226 +SHA256 (mafft-6.903-without-extensions-src.tgz) = d96326aecdb1f86b63779312c4a6d8f719f32786396567c1d1829341fc6dbcc8 +SIZE (mafft-6.903-without-extensions-src.tgz) = 359536 diff --git a/biology/mafft/pkg-descr b/biology/mafft/pkg-descr index 5c89ce1da345..3a569feb4376 100644 --- a/biology/mafft/pkg-descr +++ b/biology/mafft/pkg-descr @@ -5,8 +5,12 @@ According to BAliBASE and other benchmark tests, L-INS-i is one of the most accurate methods currently available. MAFFT has been described: + +K. Katoh and H. Toh 2008 (Briefings in Bioinformatics 9:286-298) +Recent developments in the MAFFT multiple sequence alignment program. + K. Katoh, K. Misawa, K. Kuma and T. Miyata (Nucleic Acids Res. 30: 3059-3066, 2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. -WWW: http://align.bmr.kyushu-u.ac.jp/mafft +WWW: http://mafft.cbrc.jp/alignment/software/ diff --git a/biology/mafft/pkg-plist b/biology/mafft/pkg-plist index fe1aba731d0c..0595bf093511 100644 --- a/biology/mafft/pkg-plist +++ b/biology/mafft/pkg-plist @@ -1,31 +1,68 @@ -bin/dummy +bin/einsi +bin/fftns +bin/fftnsi +bin/ginsi +bin/linsi bin/mafft -bin/disttbfast -bin/dndblast -bin/dndfast7 -bin/dndpre -bin/dndpre2 -bin/dvtditr -bin/f2cl -bin/getlag +bin/mafft-distance +bin/mafft-einsi +bin/mafft-fftns +bin/mafft-fftnsi +bin/mafft-ginsi +bin/mafft-homologs.rb +bin/mafft-linsi +bin/mafft-nwns +bin/mafft-nwnsi bin/mafft-profile -bin/multi2hat3s -bin/pair2hat3s -bin/pairalign -bin/pairlocalalign -bin/score -bin/setcore -bin/sextet5 -bin/splitseq -bin/tbfast -bin/tbfast2 +bin/mafft-qinsi +bin/mafft-xinsi +bin/nwns +bin/nwnsi +libexec/mafft/addsingle +libexec/mafft/contrafoldwrap +libexec/mafft/countlen +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/makedirectionlist +libexec/mafft/mccaskillwrap +libexec/mafft/multi2hat3s +libexec/mafft/pair2hat3s +libexec/mafft/pairash +libexec/mafft/pairlocalalign +libexec/mafft/regtable2seq +libexec/mafft/replaceu +libexec/mafft/restoreu +libexec/mafft/rnatest +libexec/mafft/score +libexec/mafft/seq2regtable +libexec/mafft/setcore +libexec/mafft/setdirection +libexec/mafft/sextet5 +libexec/mafft/splittbfast +libexec/mafft/tbfast +libexec/mafft/version +%%PORTDOCS%%%%DOCSDIR%%/license %%PORTDOCS%%%%DOCSDIR%%/readme -%%EXAMPLESDIR%%/sample -%%EXAMPLESDIR%%/sample.fftns2 -%%EXAMPLESDIR%%/sample.fftnsi -%%EXAMPLESDIR%%/sample.gins1 -%%EXAMPLESDIR%%/sample.ginsi -%%EXAMPLESDIR%%/sample.lins1 -%%EXAMPLESDIR%%/sample.linsi +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.dpparttree +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.fftns2 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.fftnsi +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.gins1 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.ginsi +%%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 %%EXAMPLESDIR%% +@dirrm libexec/mafft