Add mafft 5.734, multiple sequence alignments based on fast Fourier

transform.

PR:		ports/93059
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>

6 files changed, 119 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 1cac172ec073..a74ce6572041 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -37,6 +37,7 @@
     SUBDIR += lamarc
     SUBDIR += libgenome
     SUBDIR += lsysexp
+    SUBDIR += mafft
     SUBDIR += migrate
     SUBDIR += molden
     SUBDIR += mopac
diff --git a/biology/mafft/Makefile b/biology/mafft/Makefile
new file mode 100644
index 000000000000..6467ac999d2c
--- /dev/null
+++ b/biology/mafft/Makefile
@@ -0,0 +1,36 @@
+# ex:ts=8
+# New ports collection makefile for:	mafft
+# Date created:				1 Feb 2006
+# Whom:					Fernan Aguero <fernan@iib.unsam.edu.ar>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	mafft
+PORTVERSION=	5.734
+CATEGORIES=	biology
+MASTER_SITES=	http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/
+DISTNAME=	${PORTNAME}-${PORTVERSION}-src
+EXTRACT_SUFX=	.tgz
+
+MAINTAINER=	fernan@iib.unsam.edu.ar
+COMMENT=	Multiple sequence alignments based on fast Fourier transform
+
+RUN_DEPENDS=	fasta34:${PORTSDIR}/biology/fasta3
+
+WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}
+BUILD_WRKSRC=	${WRKSRC}/src
+
+MAKE_ENV+=	CFLAG="${CFLAGS}"
+
+do-install:
+	${INSTALL_SCRIPT} ${WRKSRC}/scripts/mafft ${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/binaries/* ${PREFIX}/bin
+	@ ${MKDIR} ${EXAMPLESDIR}
+	${INSTALL_DATA} ${WRKSRC}/test/* ${EXAMPLESDIR}
+.if !defined(NOPORTDOCS)
+	@ ${MKDIR} ${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/readme ${DOCSDIR}
+.endif
+
+.include <bsd.port.mk>
diff --git a/biology/mafft/distinfo b/biology/mafft/distinfo
new file mode 100644
index 000000000000..a6a5286c57a3
--- /dev/null
+++ b/biology/mafft/distinfo
@@ -0,0 +1,3 @@
+MD5 (mafft-5.734-src.tgz) = 2186ffb447554163705b841c3913f2b6
+SHA256 (mafft-5.734-src.tgz) = 2bf8e274f0200a0fb78a4aa61d800699da2071f0d3cb87701c37b33f3b038168
+SIZE (mafft-5.734-src.tgz) = 439184
diff --git a/biology/mafft/files/patch-Makefile b/biology/mafft/files/patch-Makefile
new file mode 100644
index 000000000000..9f59f1403ce4
--- /dev/null
+++ b/biology/mafft/files/patch-Makefile
@@ -0,0 +1,39 @@
+--- src/Makefile.orig	Wed Aug 31 06:58:17 2005
++++ src/Makefile	Sun Feb  5 01:07:37 2006
+@@ -1,8 +1,7 @@
+-PREFIX = \/usr\/local\/lib\/mafft
+ #CC = gcc  -O2  -g -pg -static
+ #CC = gcc    -mno-cygwin -O3
+ #CC = gcc -O3   -mcpu=970 -mtune=970 -mpowerpc64 -mpowerpc-gpopt -falign-loops=16 -falign-functions=16 -falign-labels=16 -falign-jumps=16
+-CC = gcc -O3 
++#CC = gcc -O3 
+ #CC = gcc  -g -O0 
+ PROGS = dvtditr dndfast7 dndblast sextet5 pairalign pairlocalalign \
+         disttbfast tbfast tbfast2 mafft-profile f2cl \
+@@ -71,19 +70,19 @@
+ 	@echo done.
+ 
+ fftns: fftns.tmpl
+-	sed "s/_PREFIX/$(PREFIX)/" fftns.tmpl  > fftns
++	sed "s,_PREFIX,$(PREFIX)," fftns.tmpl  > fftns
+ fftnsi: fftnsi.tmpl
+-	sed "s/_PREFIX/$(PREFIX)/" fftnsi.tmpl > fftnsi
++	sed "s,_PREFIX,$(PREFIX)," fftnsi.tmpl > fftnsi
+ fftnsrough: fftnsrough.tmpl
+-	sed "s/_PREFIX/$(PREFIX)/" fftnsrough.tmpl  > fftnsrough
++	sed "s,_PREFIX,$(PREFIX)," fftnsrough.tmpl  > fftnsrough
+ nwns: nwns.tmpl
+-	sed "s/_PREFIX/$(PREFIX)/" nwns.tmpl   > nwns
++	sed "s,_PREFIX,$(PREFIX)," nwns.tmpl   > nwns
+ nwnsi: nwnsi.tmpl
+-	sed "s/_PREFIX/$(PREFIX)/" nwnsi.tmpl  > nwnsi
++	sed "s,_PREFIX,$(PREFIX)," nwnsi.tmpl  > nwnsi
+ nwnsrough: nwnsrough.tmpl
+-	sed "s/_PREFIX/$(PREFIX)/" nwnsrough.tmpl  > nwnsrough
++	sed "s,_PREFIX,$(PREFIX)," nwnsrough.tmpl  > nwnsrough
+ mafft: mafft.tmpl
+-	sed "s/_PREFIX/$(PREFIX)/" mafft.tmpl  > mafft
++	sed "s,_PREFIX,$(PREFIX)," mafft.tmpl  > mafft
+ 
+ mltaln.h : functions.h
+ 	touch mltaln.h
diff --git a/biology/mafft/pkg-descr b/biology/mafft/pkg-descr
new file mode 100644
index 000000000000..6802110a357d
--- /dev/null
+++ b/biology/mafft/pkg-descr
@@ -0,0 +1,12 @@
+MAFFT offers a range of multiple alignment strategies, L-INS-i
+(accurate; recommended for <200 sequences), FFT-NS-i (standard speed and
+accuracy), FFT-NS-2 (fast; recommended for >2,000 sequences), etc.
+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, 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://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/
diff --git a/biology/mafft/pkg-plist b/biology/mafft/pkg-plist
new file mode 100644
index 000000000000..10d16212c3ef
--- /dev/null
+++ b/biology/mafft/pkg-plist
@@ -0,0 +1,28 @@
+bin/mafft
+bin/disttbfast
+bin/dndblast
+bin/dndfast7
+bin/dndpre
+bin/dndpre2
+bin/dvtditr
+bin/f2cl
+bin/getlag
+bin/mafft-profile
+bin/pairalign
+bin/pairlocalalign
+bin/score
+bin/setcore
+bin/sextet5
+bin/splitseq
+bin/tbfast
+bin/tbfast2
+%%PORTDOCS%%%%DOCSDIR%%/readme
+%%EXAMPLESDIR%%/sample
+%%EXAMPLESDIR%%/sample.fftns2
+%%EXAMPLESDIR%%/sample.fftnsi
+%%EXAMPLESDIR%%/sample.gins1
+%%EXAMPLESDIR%%/sample.ginsi
+%%EXAMPLESDIR%%/sample.lins1
+%%EXAMPLESDIR%%/sample.linsi
+%%PORTDOCS%%@dirrm %%DOCSDIR%%
+@dirrm %%EXAMPLESDIR%%