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# Created by: 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
USES= perl5
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
NO_STAGE= yes
OPTIONS_DEFINE= DOCS EXAMPLES
.include <bsd.port.options.mk>
.if ${PORT_OPTIONS:MEXAMPLES}
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 ${PORT_OPTIONS:MEXAMPLES}
@${MKDIR} ${EXAMPLESDIR}
.for dir in ${EXAMPLES}
@${CP} -R ${WRKSRC}/${dir} ${EXAMPLESDIR}
.endfor
.endif
.if ${PORT_OPTIONS:MDOCS}
@${MKDIR} ${DOCSDIR}
.for f in ${PORTDOCS}
@${INSTALL_DATA} ${WRKSRC}/${f} ${DOCSDIR}
.endfor
.endif
.if ! ${PORT_OPTIONS:MEXAMPLES}
@${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>
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