head	1.3;
access;
symbols
	RELEASE_8_3_0:1.2
	RELEASE_9_0_0:1.2
	RELEASE_7_4_0:1.1
	RELEASE_8_2_0:1.1
	RELEASE_6_EOL:1.1
	RELEASE_8_1_0:1.1
	RELEASE_7_3_0:1.1;
locks; strict;
comment	@# @;


1.3
date	2012.11.17.05.54.53;	author svnexp;	state Exp;
branches;
next	1.2;

1.2
date	2011.06.09.16.33.21;	author jlaffaye;	state Exp;
branches;
next	1.1;

1.1
date	2009.11.07.01.23.58;	author amdmi3;	state Exp;
branches;
next	;


desc
@@


1.3
log
@Switch exporter over
@
text
@# New ports collection makefile for:	velvet
# Date created:		27 Oct 2009
# Whom:			Motomichi Matsuzaki <mzaki@@m.u-tokyo.ac.jp>
#
# $FreeBSD: head/biology/velvet/Makefile 300895 2012-07-14 12:56:14Z beat $
#

PORTNAME=	velvet
PORTVERSION=	1.1.04
CATEGORIES=	biology
MASTER_SITES=	http://www.ebi.ac.uk/~zerbino/velvet/
DISTNAME=	${PORTNAME}_${PORTVERSION}
EXTRACT_SUFX=	.tgz

MAINTAINER=	mzaki@@m.u-tokyo.ac.jp
COMMENT=	Sequence assembler for very short reads

USE_GMAKE=	yes
ALL_TARGET=	default

MAXKMERLENGTH?=	31
VELVET_CATEGORIES?=	2
MAKE_ENV+=	MAXKMERLENGTH=${MAXKMERLENGTH} CATEGORIES=${VELVET_CATEGORIES}

USE_PERL5_RUN=	yes

BINARIES=	velvetg velveth
SCRIPTS=	shuffleSequences_fasta.pl shuffleSequences_fastq.pl \
		contrib/VelvetOptimiser-2.1.7/VelvetOptimiser.pl \
		contrib/afg_handling/asmbly_splitter.pl \
		contrib/afg_handling/snp_view.pl \
		contrib/columbus_scripts/enlarge_exons.pl \
		contrib/columbus_scripts/gff2fasta.pl \
		contrib/columbus_scripts/merge_gtf_exons.pl \
		contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl \
		contrib/extractContigReads/extractContigReads.pl \
		contrib/fasta2agp/fasta2agp.pl \
		contrib/observed-insert-length.pl/observed-insert-length.pl \
		contrib/select_paired/select_paired.pl \
		contrib/show_repeats/show_repeats.pl
PERLMOD_DIRS=	contrib/VelvetOptimiser-2.1.7/VelvetOpt
PERLMOD_FILES=	contrib/VelvetOptimiser-2.1.7/VelvetOpt/Assembly.pm \
		contrib/VelvetOptimiser-2.1.7/VelvetOpt/Utils.pm \
		contrib/VelvetOptimiser-2.1.7/VelvetOpt/gwrap.pm \
		contrib/VelvetOptimiser-2.1.7/VelvetOpt/hwrap.pm

.if !defined(WITHOUT_PYTHON)
USE_PYTHON=	yes
SCRIPTS+=	contrib/AssemblyAssembler1.3/AssemblyAssembler1.3.py
.endif

.for f in ${BINARIES} ${SCRIPTS}
PLIST_FILES+=	bin/${f:T}
.endfor
.for d in ${PERLMOD_DIRS}
PLIST_DIRS+=	%%SITE_PERL%%/${d:T}
.endfor
.for f in ${PERLMOD_FILES}
PLIST_FILES+=	%%SITE_PERL%%/${f:H:T}/${f:T}
.endfor

PORTDOCS=	ChangeLog Manual.pdf Columbus_manual.pdf

post-patch:
.for f in ${SCRIPTS}
	${REINPLACE_CMD} -e s,#!/usr/bin/perl,${PERL}, ${WRKSRC}/${f}
.endfor
.if !defined(WITHOUT_PYTHON)
	${REINPLACE_CMD} -e s,#!/usr/bin/python,${PYTHON_CMD}, ${WRKSRC}/contrib/AssemblyAssembler1.3/AssemblyAssembler1.3.py
.endif

do-install:
.for f in ${BINARIES}
	${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin
.endfor
.for f in ${SCRIPTS}
	${INSTALL_SCRIPT} ${WRKSRC}/${f} ${PREFIX}/bin/${f:T}
.endfor
.for d in ${PERLMOD_DIRS}
	${MKDIR} ${PREFIX}/${SITE_PERL_REL}/${d:T}
.endfor
.for f in ${PERLMOD_FILES}
	${INSTALL_DATA} ${WRKSRC}/${f} ${PREFIX}/${SITE_PERL_REL}/${f:H:T}/${f:T}
.endfor
.if !defined(NOPORTDOCS)
	${MKDIR} ${DOCSDIR}
.for f in ${PORTDOCS}
	${INSTALL_MAN} ${WRKSRC}/${f} ${DOCSDIR}
.endfor
.endif

.include <bsd.port.mk>
@


1.2
log
@Update to 1.1.04

PR:		ports/157527
Submitted by:	Motomichi Matsuzaki <mzaki@@m.u-tokyo.ac.jp>
Approved by:	bapt (mentor)
@
text
@d5 1
a5 1
# $FreeBSD$
@


1.1
log
@Velvet is a de novo genomic assembler specially designed for short read
sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino
and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI).

Citation:

Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
D.R. Zerbino and E. Birney. Genome Research 18: 821-829 (2008)

WWW: http://www.ebi.ac.uk/~zerbino/velvet/

PR:		140147
Submitted by:	Motomichi Matsuzaki <mzaki@@m.u-tokyo.ac.jp>
@
text
@d9 1
a9 1
PORTVERSION=	0.7.55
d22 2
a23 1
MAKE_ENV+=	MAXKMERLENGTH=${MAXKMERLENGTH}
d28 2
a29 1
SCRIPTS=	contrib/VelvetOptimiser/VelvetOptimiser.pl \
d32 3
d36 1
a37 1
		contrib/extractContigReads/extractContigReads.pl \
d39 7
a45 6
		contrib/shuffleSequences_fasta/shuffleSequences_fasta.pl
PERLMOD_DIRS=	contrib/VelvetOptimiser/VelvetOpt
PERLMOD_FILES=	contrib/VelvetOptimiser/VelvetOpt/Assembly.pm \
		contrib/VelvetOptimiser/VelvetOpt/Utils.pm \
		contrib/VelvetOptimiser/VelvetOpt/gwrap.pm \
		contrib/VelvetOptimiser/VelvetOpt/hwrap.pm
d49 1
a49 1
SCRIPTS+=	contrib/layout/graph2.py
d62 1
a62 1
PORTDOCS=	ChangeLog Manual.pdf
d69 1
a69 1
	(IFS=''; ${REINPLACE_CMD} -e `${ECHO} '1i\'; ${ECHO} '#!${PYTHON_CMD}'` ${WRKSRC}/contrib/layout/graph2.py)
a71 3
post-build:
	${REINPLACE_CMD} -e s,%%MAXKMERLENGTH%%,${MAXKMERLENGTH},g ${WRKSRC}/contrib/VelvetOptimiser/VelvetOptimiser.pl

@

