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Date:      Mon, 16 Jul 2012 15:22:47 -0700 (MST)
From:      "Reed A. Cartwright" <cartwright@asu.edu>
To:        FreeBSD-gnats-submit@FreeBSD.org
Subject:   ports/169920: Update biology/mafft to latest version
Message-ID:  <201207162222.q6GMMlaC035579@herschel.biodesign.asu.edu>
Resent-Message-ID: <201207162250.q6GMo58e096602@freefall.freebsd.org>

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>Number:         169920
>Category:       ports
>Synopsis:       Update biology/mafft to latest version
>Confidential:   no
>Severity:       non-critical
>Priority:       medium
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          update
>Submitter-Id:   current-users
>Arrival-Date:   Mon Jul 16 22:50:04 UTC 2012
>Closed-Date:
>Last-Modified:
>Originator:     Reed A. Cartwright
>Release:        FreeBSD 9.0-RELEASE-p3 amd64
>Organization:
Arizona State University
>Environment:
System: FreeBSD herschel.biodesign.asu.edu 9.0-RELEASE-p3 FreeBSD 9.0-RELEASE-p3 #0: Tue Jun 12 02:52:29 UTC 2012 root@amd64-builder.daemonology.net:/usr/obj/usr/src/sys/GENERIC amd64

>Description:

The port biology/mafft is out of date and does not run successfully on recent 
version of FreeBSD.
	
>How-To-Repeat:
>Fix:

A Patch is attached to upgrade the port to version 6.903.  If desired, I am willing 
to take over ownership of the port.

--- biolog.mafft.patch begins here ---
diff /usr/ports/biology/mafft.orig/Makefile /usr/ports/biology/mafft/Makefile
10c10
< PORTVERSION=	5.743
---
> PORTVERSION=	6.903
12,13c12,13
< 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
17c17,19
< COMMENT=	Multiple sequence alignments based on fast Fourier transform
---
> COMMENT=	Multiple alignment program for amino acid or nucleotide sequences
> 
> LICENSE=	BSD
21,22c23,38
< WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}
< BUILD_WRKSRC=	${WRKSRC}/src
---
> WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}-without-extensions
> BUILD_WRKSRC=	${WRKSRC}/core
> 
> USE_GMAKE=	yes
> 
> MAN1=		mafft.1 mafft-homologs.1
> 
> LIBEXEC_FILES=	dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \
> 		pair2hat3s multi2hat3s rnatest pairash addsingle splittbfast \
> 		disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap \
> 		countlen seq2regtable regtable2seq score getlag dndpre dndpre2 \
> 		setcore replaceu restoreu setdirection makedirectionlist version
> SCRIPT_FILES=	mafft mafft-homologs.rb
> LN_FILES=	einsi fftns fftnsi ginsi linsi mafft-einsi mafft-fftns \
> 		mafft-fftnsi mafft-ginsi mafft-linsi mafft-nwns mafft-nwnsi \
> 		mafft-qinsi mafft-xinsi nwns nwnsi
24c40
< MAKE_ENV+=	CFLAG="${CFLAGS}"
---
> .include <bsd.port.pre.mk>
27,28c43,48
< 	@${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
31,33c51,66
< 	${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}
36c69
< 	@ ${MKDIR} ${DOCSDIR}
---
> 	@${MKDIR} ${DOCSDIR}
37a71
> 	${INSTALL_DATA} ${WRKSRC}/license ${DOCSDIR}
40c74
< .include <bsd.port.mk>
---
> .include <bsd.port.post.mk>
diff /usr/ports/biology/mafft.orig/distinfo /usr/ports/biology/mafft/distinfo
1,2c1,2
< 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 /usr/ports/biology/mafft.orig/pkg-descr /usr/ports/biology/mafft/pkg-descr
7a8,11
> 
> K. Katoh and H. Toh 2008 (Briefings in Bioinformatics 9:286-298)
> Recent developments in the MAFFT multiple sequence alignment program.
> 
12c16
< WWW: http://align.bmr.kyushu-u.ac.jp/mafft
---
> WWW: http://mafft.cbrc.jp/alignment/software/
diff /usr/ports/biology/mafft.orig/pkg-plist /usr/ports/biology/mafft/pkg-plist
1c1,5
< bin/dummy
---
> bin/einsi
> bin/fftns
> bin/fftnsi
> bin/ginsi
> bin/linsi
3,10c7,15
< 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
12,21c17,52
< 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
23,29c54,66
< %%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%%
31c68
< @dirrm %%EXAMPLESDIR%%
---
> @dirrm libexec/mafft
--- biolog.mafft.patch ends here ---


>Release-Note:
>Audit-Trail:
>Unformatted:



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