head	1.3;
access;
symbols
	RELEASE_8_3_0:1.2
	RELEASE_9_0_0:1.2
	RELEASE_7_4_0:1.2
	RELEASE_8_2_0:1.2
	RELEASE_6_EOL:1.2
	RELEASE_8_1_0:1.2
	RELEASE_7_3_0:1.2
	RELEASE_8_0_0:1.2
	RELEASE_7_2_0:1.2
	RELEASE_7_1_0:1.2
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	RELEASE_5_EOL:1.2;
locks; strict;
comment	@# @;


1.3
date	2012.11.17.05.54.52;	author svnexp;	state Exp;
branches;
next	1.2;

1.2
date	2008.05.25.23.05.10;	author edwin;	state Exp;
branches;
next	1.1;

1.1
date	2008.05.24.07.04.45;	author edwin;	state Exp;
branches;
next	;


desc
@@


1.3
log
@Switch exporter over
@
text
@# New ports collection makefile for:	phred
# Date created:		6 December 2007
# Whom:			Motomichi Matsuzaki <mzaki@@biol.s.u-tokyo.ac.jp>
#
# $FreeBSD: head/biology/phred/Makefile 300895 2012-07-14 12:56:14Z beat $
#

PORTNAME=	phred
PORTVERSION=	0.020425.c
CATEGORIES=	biology
MASTER_SITES=	# put the tarball manually
DISTNAME=	${PORTNAME}-dist-${PORTVERSION:S/0.//}-acd
EXTRACT_SUFX=	.tar.Z

MAINTAINER=	mzaki@@biol.s.u-tokyo.ac.jp
COMMENT=	Base calling and quality value assignment on DNA sequencing

RESTRICTED=	Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use.
.if defined(PACKAGE_BUILDING)
IGNORE=		distribution files must be obtained via the authors
.endif

NO_WRKSUBDIR=	yes

ALL_TARGET=	phred daev

BINMODE=	0111	# avoid copying binaries as required by the agreement
BINARIES=	phred daev
.for f in ${BINARIES}
PLIST_FILES+=	bin/${f}
.endfor

DATADIR=	${PREFIX}/etc/PhredPar
DATAFILES=	phredpar.dat
.for f in ${DATAFILES}
PORTDATA+=	${f}.dist
.endfor

PORTDOCS=	NEWS PHRED.DOC DAEV.DOC

.include <bsd.port.pre.mk>

.for f in ${DISTFILES}
.if !exists(${DISTDIR}/${f})
IGNORE=	you must request the source code \(${f}\) via e-mail, place it manually in ${DISTDIR}, and then try it again
.endif
.endfor

do-install:
.for f in ${BINARIES}
	@@${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin/
.endfor
	@@${MKDIR} ${DATADIR}
.for f in ${DATAFILES}
	@@${INSTALL_DATA} ${WRKSRC}/${f} ${DATADIR}/${f}.dist
.endfor
.if !defined(NOPORTDOCS)
	@@${MKDIR} ${DOCSDIR}
.for f in ${PORTDOCS}
	@@${INSTALL_DATA} ${WRKSRC}/${f} ${DOCSDIR}
.endfor
.endif
	@@${ECHO} "---------------------------------------------------------------------------"
	@@${ECHO} "You must set PHRED_PARAMETER_FILE environment variable."
	@@${ECHO} ""
	@@${ECHO} "The default parameter file in the distribution is located at:"
	@@${ECHO} "  ${DATADIR}/phredpar.dat.dist"
	@@${ECHO} "---------------------------------------------------------------------------"

.include <bsd.port.post.mk>
@


1.2
log
@Teach the building cluster that these ports are not to be build
@
text
@d5 1
a5 1
# $FreeBSD$
@


1.1
log
@New port: biology/consed viewing and editing workbench for sequence
assembly

	Consed is a tool for viewing, editing, and finishing sequence
	assemblies.

	The port is constituted of 4 parts:
	biology/phred: base caller with quality evaluation
	biology/phrap: sequence assembler for shotgun sequencing
	biology/consed: workbench
	biology/phd2fasta: small utility

	All these can be used separately; however, most function
	of consed depends on the others.

	Although these programs are licensed freely for academic
	and nonprofit purposes, users have to contact the authors
	to get the softwares.
	Phred (including phd2fasta) and phrap are emailed,
	and consed can be downloaded to a restricted IP address.
	For commercial users, the licensing fee is ca. $10,000 at
	the time of writing.

PR:		ports/118548
Submitted by:	Motomichi Matsuzaki <mzaki@@biol.s.u-tokyo.ac.jp>
@
text
@d19 3
@

