- Update to version 6.903

PR:		ports/169920
Submitted by:	"Reed A. Cartwright" <cartwright@asu.edu>
Approved by:	maintainer (timeout, 21 days)

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
+
+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
 
-MAKE_ENV+=	CFLAG="${CFLAGS}"
+.include <bsd.port.pre.mk>
 
 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 <bsd.port.mk>
+.include <bsd.port.post.mk>
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