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# Created by: Fernan Aguero <fernan@iib.unsam.edu.ar>
# $FreeBSD$
PORTNAME= mafft
PORTVERSION= 6.903
CATEGORIES= biology
MASTER_SITES= http://mafft.cbrc.jp/alignment/software/
DISTNAME= ${PORTNAME}-${PORTVERSION}-without-extensions-src
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
WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}-without-extensions
BUILD_WRKSRC= ${WRKSRC}/core
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
NO_STAGE= yes
.include <bsd.port.pre.mk>
.if ${ARCH} == "sparc64"
BROKEN= Does not install on sparc64: depends on thread-local storage
.endif
post-patch:
@${REINPLACE_CMD} -e 's|-lpthread|${PTHREAD_LIBS}|' \
-e 's|^MANDIR = .*$$|MANDIR = $$(MANPREFIX)/man/man1|' \
-e 's|^PREFIX = .*$$||' \
-e 's|^CC = .*$$||' \
-e 's|^CFLAGS = .*$$||' \
${BUILD_WRKSRC}/Makefile
do-install:
@${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}
${INSTALL_DATA} ${WRKSRC}/readme ${DOCSDIR}
${INSTALL_DATA} ${WRKSRC}/license ${DOCSDIR}
.endif
.include <bsd.port.post.mk>
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