- Update to version 6.903
PR: ports/169920 Submitted by: "Reed A. Cartwright" <cartwright@asu.edu> Approved by: maintainer (timeout, 21 days)
This commit is contained in:
Michael Scheidell
parent
bd83955025
commit
2c946497ba
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=302236
@ -7,34 +7,68 @@
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#
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PORTNAME= mafft
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PORTVERSION= 5.743
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PORTVERSION= 6.903
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CATEGORIES= biology
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MASTER_SITES= http://align.bmr.kyushu-u.ac.jp/mafft/software/
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DISTNAME= ${PORTNAME}-${PORTVERSION}-src
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MASTER_SITES= http://mafft.cbrc.jp/alignment/software/
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DISTNAME= ${PORTNAME}-${PORTVERSION}-without-extensions-src
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EXTRACT_SUFX= .tgz
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MAINTAINER= fernan@iib.unsam.edu.ar
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COMMENT= Multiple sequence alignments based on fast Fourier transform
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COMMENT= Multiple alignment program for amino acid or nucleotide sequences
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LICENSE= BSD
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RUN_DEPENDS= lav2ps:${PORTSDIR}/biology/fasta3
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WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}
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BUILD_WRKSRC= ${WRKSRC}/src
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WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}-without-extensions
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BUILD_WRKSRC= ${WRKSRC}/core
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MAKE_ENV+= CFLAG="${CFLAGS}"
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USE_GMAKE= yes
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MAN1= mafft.1 mafft-homologs.1
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LIBEXEC_FILES= dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \
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pair2hat3s multi2hat3s rnatest pairash addsingle splittbfast \
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disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap \
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countlen seq2regtable regtable2seq score getlag dndpre dndpre2 \
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setcore replaceu restoreu setdirection makedirectionlist version
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SCRIPT_FILES= mafft mafft-homologs.rb
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LN_FILES= einsi fftns fftnsi ginsi linsi mafft-einsi mafft-fftns \
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mafft-fftnsi mafft-ginsi mafft-linsi mafft-nwns mafft-nwnsi \
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mafft-qinsi mafft-xinsi nwns nwnsi
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.include <bsd.port.pre.mk>
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post-patch:
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@${REINPLACE_CMD} -E 's,^(CC|PREFIX) =,\1 ?=,' \
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${WRKSRC}/src/Makefile
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@${REINPLACE_CMD} -e 's|-lpthread|${PTHREAD_LIBS}|' \
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-e 's|^MANDIR = .*$$|MANDIR = $$(MANPREFIX)/man/man1|' \
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-e 's|^PREFIX = .*$$||' \
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-e 's|^CC = .*$$||' \
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-e 's|^CFLAGS = .*$$||' \
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${BUILD_WRKSRC}/Makefile
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do-install:
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${INSTALL_SCRIPT} ${WRKSRC}/scripts/mafft ${PREFIX}/bin
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${INSTALL_PROGRAM} ${WRKSRC}/binaries/* ${PREFIX}/bin
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@ ${MKDIR} ${EXAMPLESDIR}
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@${MKDIR} ${PREFIX}/libexec/${PORTNAME}
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.for exec in ${LIBEXEC_FILES}
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${INSTALL_PROGRAM} ${WRKSRC}/binaries/${exec} ${PREFIX}/libexec/${PORTNAME}
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.endfor
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.for exec in ${SCRIPT_FILES}
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${INSTALL_SCRIPT} ${WRKSRC}/scripts/${exec} ${PREFIX}/bin
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.endfor
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.for exec in ${LN_FILES}
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${LN} -fs ${PREFIX}/bin/mafft ${PREFIX}/bin/${exec}
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.endfor
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${LN} -fs ${PREFIX}/libexec/${PORTNAME}/mafft-distance ${PREFIX}/bin/mafft-distance
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${LN} -fs ${PREFIX}/libexec/${PORTNAME}/mafft-profile ${PREFIX}/bin/mafft-profile
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.for man in ${MAN1}
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${INSTALL_MAN} ${WRKSRC}/binaries/${man} ${MAN1PREFIX}/man/man1
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.endfor
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@${MKDIR} ${EXAMPLESDIR}
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${INSTALL_DATA} ${WRKSRC}/test/* ${EXAMPLESDIR}
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.if !defined(NOPORTDOCS)
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@ ${MKDIR} ${DOCSDIR}
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@${MKDIR} ${DOCSDIR}
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${INSTALL_DATA} ${WRKSRC}/readme ${DOCSDIR}
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${INSTALL_DATA} ${WRKSRC}/license ${DOCSDIR}
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.endif
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.include <bsd.port.mk>
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.include <bsd.port.post.mk>
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@ -1,2 +1,2 @@
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SHA256 (mafft-5.743-src.tgz) = 7bf0d450fea1d44fafee27c29c74b3ae4247ad0075b41729d9dc935e2a88de66
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SIZE (mafft-5.743-src.tgz) = 280226
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SHA256 (mafft-6.903-without-extensions-src.tgz) = d96326aecdb1f86b63779312c4a6d8f719f32786396567c1d1829341fc6dbcc8
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SIZE (mafft-6.903-without-extensions-src.tgz) = 359536
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@ -5,8 +5,12 @@ According to BAliBASE and other benchmark tests, L-INS-i is one of the
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most accurate methods currently available.
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MAFFT has been described:
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K. Katoh and H. Toh 2008 (Briefings in Bioinformatics 9:286-298)
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Recent developments in the MAFFT multiple sequence alignment program.
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K. Katoh, K. Misawa, K. Kuma and T. Miyata (Nucleic Acids Res. 30:
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3059-3066, 2002) MAFFT: a novel method for rapid multiple sequence
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alignment based on fast Fourier transform.
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WWW: http://align.bmr.kyushu-u.ac.jp/mafft
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WWW: http://mafft.cbrc.jp/alignment/software/
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@ -1,31 +1,68 @@
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bin/dummy
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bin/einsi
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bin/fftns
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bin/fftnsi
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bin/ginsi
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bin/linsi
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bin/mafft
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bin/disttbfast
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bin/dndblast
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bin/dndfast7
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bin/dndpre
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bin/dndpre2
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bin/dvtditr
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bin/f2cl
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bin/getlag
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bin/mafft-distance
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bin/mafft-einsi
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bin/mafft-fftns
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bin/mafft-fftnsi
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bin/mafft-ginsi
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bin/mafft-homologs.rb
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bin/mafft-linsi
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bin/mafft-nwns
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bin/mafft-nwnsi
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bin/mafft-profile
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bin/multi2hat3s
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bin/pair2hat3s
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bin/pairalign
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bin/pairlocalalign
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bin/score
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bin/setcore
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bin/sextet5
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bin/splitseq
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bin/tbfast
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bin/tbfast2
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bin/mafft-qinsi
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bin/mafft-xinsi
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bin/nwns
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bin/nwnsi
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libexec/mafft/addsingle
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libexec/mafft/contrafoldwrap
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libexec/mafft/countlen
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libexec/mafft/disttbfast
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libexec/mafft/dndblast
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libexec/mafft/dndfast7
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libexec/mafft/dndpre
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libexec/mafft/dndpre2
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libexec/mafft/dvtditr
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libexec/mafft/f2cl
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libexec/mafft/getlag
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libexec/mafft/mafft-distance
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libexec/mafft/mafft-profile
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libexec/mafft/makedirectionlist
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libexec/mafft/mccaskillwrap
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libexec/mafft/multi2hat3s
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libexec/mafft/pair2hat3s
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libexec/mafft/pairash
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libexec/mafft/pairlocalalign
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libexec/mafft/regtable2seq
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libexec/mafft/replaceu
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libexec/mafft/restoreu
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libexec/mafft/rnatest
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libexec/mafft/score
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libexec/mafft/seq2regtable
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libexec/mafft/setcore
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libexec/mafft/setdirection
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libexec/mafft/sextet5
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libexec/mafft/splittbfast
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libexec/mafft/tbfast
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libexec/mafft/version
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%%PORTDOCS%%%%DOCSDIR%%/license
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%%PORTDOCS%%%%DOCSDIR%%/readme
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%%EXAMPLESDIR%%/sample
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%%EXAMPLESDIR%%/sample.fftns2
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%%EXAMPLESDIR%%/sample.fftnsi
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%%EXAMPLESDIR%%/sample.gins1
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%%EXAMPLESDIR%%/sample.ginsi
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%%EXAMPLESDIR%%/sample.lins1
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%%EXAMPLESDIR%%/sample.linsi
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.dpparttree
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.fftns2
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.fftnsi
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.gins1
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.ginsi
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.lins1
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.linsi
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.parttree
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna.qinsi
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna.xinsi
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%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
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%%PORTDOCS%%@dirrm %%DOCSDIR%%
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@dirrm %%EXAMPLESDIR%%
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@dirrm libexec/mafft
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