1 files changed, 104 insertions, 0 deletions

diff --git a/biology/consed/Makefile b/biology/consed/Makefile
new file mode 100644
index 000000000000..15700c79f7bf
--- /dev/null
+++ b/biology/consed/Makefile
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+# New ports collection makefile for:	phred
+# Date created:		8 July 2005
+# Whom:			Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
+#
+# $FreeBSD$
+#
+
+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_XLIB=	yes
+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.
+
+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>