head	1.4;
access;
symbols
	RELEASE_8_3_0:1.3
	RELEASE_9_0_0:1.3
	RELEASE_7_4_0:1.3
	RELEASE_8_2_0:1.3
	RELEASE_6_EOL:1.3
	RELEASE_8_1_0:1.3
	RELEASE_7_3_0:1.3
	RELEASE_8_0_0:1.3
	RELEASE_7_2_0:1.3
	RELEASE_7_1_0:1.2
	RELEASE_6_4_0:1.2
	RELEASE_5_EOL:1.2;
locks; strict;
comment	@# @;


1.4
date	2012.11.17.05.54.51;	author svnexp;	state Exp;
branches;
next	1.3;

1.3
date	2009.03.19.17.28.31;	author bsam;	state Exp;
branches;
next	1.2;

1.2
date	2008.05.25.23.05.09;	author edwin;	state Exp;
branches;
next	1.1;

1.1
date	2008.05.24.07.00.37;	author edwin;	state Exp;
branches;
next	;


desc
@@


1.4
log
@Switch exporter over
@
text
@# New ports collection makefile for:	phred
# Date created:		8 July 2005
# Whom:			Motomichi Matsuzaki <mzaki@@biol.s.u-tokyo.ac.jp>
#
# $FreeBSD: head/biology/consed/Makefile 300895 2012-07-14 12:56:14Z beat $
#

PORTNAME=	consed
PORTVERSION=	16.0
CATEGORIES=	biology
MASTER_SITES=	http://www.phrap.org/consed/distributions/${PORTVERSION}/
DISTNAME=	${PORTNAME}_linux
EXTRACT_SUFX=	.tar.Z

MAINTAINER=	mzaki@@biol.s.u-tokyo.ac.jp
COMMENT=	A graphical tool for editing Phrap assemblies

RUN_DEPENDS=	phred:${PORTSDIR}/biology/phred \
		phrap:${PORTSDIR}/biology/phrap \
		phd2fasta:${PORTSDIR}/biology/phd2fasta

USE_PERL5=	yes
USE_LINUX=	yes
USE_LINUX_APPS=	xorglibs
ONLY_FOR_ARCHS=	i386 amd64

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

NO_WRKSUBDIR=	yes

BUILD_WRKSRC=	${WRKSRC}/misc/mktrace
ALL_TARGET=	mktrace

BINARIES=	consed mktrace sffinfo sff2scf
CONTRIBS=	ace2OligosWithComments.perl ace2fof \
		aceContigs2Phds.perl acestatus.pl export_cons \
		mergeAces.perl recover_consensus_tags revert_fof
SCRIPTS=	ace2Fasta.perl ace2Oligos.perl addReads2Consed.perl \
		amplifyTranscripts.perl catPhdFiles.perl \
		countEditedBases.perl determineReadTypes.perl fasta2Phd.perl \
		findSequenceMatchesForConsed.perl lib2Phd.perl \
		orderPrimerPairs.perl phd2Ace.perl phredPhrap removeReads \
		revertToUneditedRead tagRepeats.perl transferConsensusTags.perl
.for f in ${BINARIES} ${CONTRIBS} ${SCRIPTS}
PLIST_FILES+=	bin/${f}
.endfor

DATADIR=	${PREFIX}/lib/screenLibs
DATAFILES=	primerCloneScreen.seq primerSubcloneScreen.seq \
		repeats.fasta singleVectorForRestrictionDigest.fasta
NULLFILES=	vector.seq
.for f in ${DATAFILES} ${NULLFILES}
PORTDATA+=	${f}.dist
.endfor
PORTDOCS=	README.txt

.if defined(WITH_EXAMPLES)
EXAMPLES=	standard autofinish assembly_view polyphred
PLIST=		${PKGDIR}/pkg-plist.examples
.endif

post-build:
	(cd ${WRKSRC}/misc/454; ${CC} ${CFLAGS} sffinfo.c -o sffinfo)
	(cd ${WRKSRC}/misc/454; ${CC} ${CFLAGS} sff2scf.c -o sff2scf)

do-install:
	@@${INSTALL_PROGRAM} ${WRKSRC}/consed_linux2.4 ${PREFIX}/bin/consed
	@@${INSTALL_PROGRAM} ${BUILD_WRKSRC}/mktrace ${PREFIX}/bin/
	@@${INSTALL_PROGRAM} ${WRKSRC}/misc/454/sffinfo ${PREFIX}/bin/
	@@${INSTALL_PROGRAM} ${WRKSRC}/misc/454/sff2scf ${PREFIX}/bin/
.for f in ${BINARIES}
	@@${CHMOD} a-r ${PREFIX}/bin/${f}
.endfor
.for f in ${CONTRIBS}
	@@${INSTALL_SCRIPT} ${WRKSRC}/contributions/${f} ${PREFIX}/bin/
.endfor
.for f in ${SCRIPTS}
	@@${INSTALL_SCRIPT} ${WRKSRC}/scripts/${f} ${PREFIX}/bin/
.endfor
	@@${MKDIR} ${DATADIR}
.for f in ${DATAFILES}
	@@${INSTALL_DATA} ${WRKSRC}/misc/${f} ${DATADIR}/${f}.dist
.endfor
.for f in ${NULLFILES}
	@@${INSTALL_DATA} /dev/null ${DATADIR}/${f}.dist
.endfor
.if !defined(NOPORTEXAMPLES)
	@@${MKDIR} ${EXAMPLESDIR}
.for dir in ${EXAMPLES}
	@@${CP} -R ${WRKSRC}/${dir} ${EXAMPLESDIR}
.endfor
.endif
.if !defined(NOPORTDOCS)
	@@${MKDIR} ${DOCSDIR}
.for f in ${PORTDOCS}
	@@${INSTALL_DATA} ${WRKSRC}/${f} ${DOCSDIR}
.endfor
.endif
.if !defined(WITH_EXAMPLES)
	@@${ECHO_CMD} "Examples were not installed. You can define WITH_EXAMPLES=yes to install them."
.endif
	@@${ECHO_CMD} "You must set the CONSED_HOME environment variable to '${PREFIX}'"

.include <bsd.port.mk>
@


1.3
log
@Welcome to the new linux ports infrastructure which allows using
both current (fc4) and future linux (f8) distributions at one
ports tree.

The patch contains full changes to ports/Mk files and all ports involved.
But only infrastructure is changed. The resulting packages are the same as
before. Hence no need to bump PORTREVISIONs.

The idea was taken from bsd.gnome.mk and others.

More than 130 ports are switched to follow a new linux infrastructure
introduced by changes to bsd.port.mk, bsd.linux-rpm.mk and a new
bsd.linux-apps.mk.

Thanks for all who was involved and helped me with this work.
And help from Alexander Leidinger was incredible.

Other changes are coming. Stay tuned!

PR:		ports/132510
Submitted by:	bsam (me)
Exp-run by:	portmgr (pav)
@
text
@d5 1
a5 1
# $FreeBSD$
@


1.2
log
@Teach the building cluster that these ports are not to be build
@
text
@d24 1
a24 1
USE_XLIB=	yes
@


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
@d28 3
@

