Attachment 142676 Details for Bug 189746 – mafft.diff

[patch] mafft.diff

mafft.diff (text/plain), 5.76 KB, created by cartwright on 2014-05-13 03:40:00 UTC

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Creator: cartwright

Created: 2014-05-13 03:40:00 UTC

Size: 5.76 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 353911)
>+++ Makefile	(working copy)
>@@ -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 @@
> MAINTAINER=	cartwright@asu.edu
> COMMENT=	Multiple alignment program for amino acid or nucleotide sequences
> 
>-LICENSE=	BSD
>+LICENSE=	BSD2CLAUSE
> 
>-RUN_DEPENDS=	lav2ps:${PORTSDIR}/biology/fasta3
>-
> 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 @@
> 		${BUILD_WRKSRC}/Makefile
> 
> do-install:
>-	@${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>
>Index: distinfo
>===================================================================
>--- distinfo	(revision 353911)
>+++ distinfo	(working copy)
>@@ -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
>Index: pkg-plist
>===================================================================
>--- pkg-plist	(revision 353911)
>+++ pkg-plist	(working copy)
>@@ -25,12 +25,12 @@
> 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/regtable2seq
> libexec/mafft/replaceu
> libexec/mafft/restoreu
>-libexec/mafft/rnatest
> libexec/mafft/score
> libexec/mafft/seq2regtable
> libexec/mafft/setcore
>@@ -49,14 +48,18 @@
> 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
>@@ -63,6 +66,6 @@
> %%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%%

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Attachments on bug 189746: 142676