- Update to 7.149

- Clarify LICENSE
- Stagify

PR:		189746
Submitted by:	"Reed A. Cartwright" <cartwright@asu.edu> (maintainer)

3 files changed, 35 insertions, 32 deletions

diff --git a/biology/mafft/Makefile b/biology/mafft/Makefile
index 87b2e322c596..69584afb6145 100644
--- a/biology/mafft/Makefile
+++ b/biology/mafft/Makefile
@@ -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 @@ 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
+LICENSE=	BSD2CLAUSE
 
 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 @@ post-patch:
 		${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>
diff --git a/biology/mafft/distinfo b/biology/mafft/distinfo
index b19598a0b49e..6c04f2612fe6 100644
--- a/biology/mafft/distinfo
+++ b/biology/mafft/distinfo
@@ -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
diff --git a/biology/mafft/pkg-plist b/biology/mafft/pkg-plist
index 0595bf093511..06086ea9574c 100644
--- a/biology/mafft/pkg-plist
+++ b/biology/mafft/pkg-plist
@@ -25,12 +25,12 @@ 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/mafftash_premafft.pl
 libexec/mafft/makedirectionlist
 libexec/mafft/mccaskillwrap
 libexec/mafft/multi2hat3s
@@ -40,7 +40,6 @@ libexec/mafft/pairlocalalign
 libexec/mafft/regtable2seq
 libexec/mafft/replaceu
 libexec/mafft/restoreu
-libexec/mafft/rnatest
 libexec/mafft/score
 libexec/mafft/seq2regtable
 libexec/mafft/setcore
@@ -49,20 +48,24 @@ libexec/mafft/sextet5
 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
 %%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%%