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110 lines
3.2 KiB
Makefile
110 lines
3.2 KiB
Makefile
# Created by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
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# $FreeBSD$
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PORTNAME= consed
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PORTVERSION= 16.0
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CATEGORIES= biology
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MASTER_SITES= http://www.phrap.org/consed/distributions/${PORTVERSION}/
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DISTNAME= ${PORTNAME}_linux
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EXTRACT_SUFX= .tar.Z
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MAINTAINER= mzaki@m.u-tokyo.ac.jp
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COMMENT= A graphical tool for editing Phrap assemblies
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RUN_DEPENDS= phred:${PORTSDIR}/biology/phred \
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phrap:${PORTSDIR}/biology/phrap \
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phd2fasta:${PORTSDIR}/biology/phd2fasta
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USES= perl5
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USE_LINUX= yes
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USE_LINUX_APPS= xorglibs
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ONLY_FOR_ARCHS= i386 amd64
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RESTRICTED= Redistribution is not permitted in any form. You must request access permission via e-mail to get the tarball. Free for academic use.
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.if defined(PACKAGE_BUILDING)
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IGNORE= distribution files must be obtained via the authors
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.endif
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NO_WRKSUBDIR= yes
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BUILD_WRKSRC= ${WRKSRC}/misc/mktrace
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ALL_TARGET= mktrace
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BINARIES= consed mktrace sffinfo sff2scf
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CONTRIBS= ace2OligosWithComments.perl ace2fof \
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aceContigs2Phds.perl acestatus.pl export_cons \
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mergeAces.perl recover_consensus_tags revert_fof
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SCRIPTS= ace2Fasta.perl ace2Oligos.perl addReads2Consed.perl \
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amplifyTranscripts.perl catPhdFiles.perl \
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countEditedBases.perl determineReadTypes.perl fasta2Phd.perl \
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findSequenceMatchesForConsed.perl lib2Phd.perl \
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orderPrimerPairs.perl phd2Ace.perl phredPhrap removeReads \
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revertToUneditedRead tagRepeats.perl transferConsensusTags.perl
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.for f in ${BINARIES} ${CONTRIBS} ${SCRIPTS}
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PLIST_FILES+= bin/${f}
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.endfor
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DATADIR= ${PREFIX}/lib/screenLibs
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DATAFILES= primerCloneScreen.seq primerSubcloneScreen.seq \
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repeats.fasta singleVectorForRestrictionDigest.fasta
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NULLFILES= vector.seq
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.for f in ${DATAFILES} ${NULLFILES}
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PORTDATA+= ${f}.dist
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.endfor
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PORTDOCS= README.txt
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NO_STAGE= yes
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OPTIONS_DEFINE= DOCS EXAMPLES
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.include <bsd.port.options.mk>
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.if ${PORT_OPTIONS:MEXAMPLES}
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EXAMPLES= standard autofinish assembly_view polyphred
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PLIST= ${PKGDIR}/pkg-plist.examples
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.endif
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post-build:
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(cd ${WRKSRC}/misc/454; ${CC} ${CFLAGS} sffinfo.c -o sffinfo)
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(cd ${WRKSRC}/misc/454; ${CC} ${CFLAGS} sff2scf.c -o sff2scf)
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do-install:
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@${INSTALL_PROGRAM} ${WRKSRC}/consed_linux2.4 ${PREFIX}/bin/consed
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@${INSTALL_PROGRAM} ${BUILD_WRKSRC}/mktrace ${PREFIX}/bin/
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@${INSTALL_PROGRAM} ${WRKSRC}/misc/454/sffinfo ${PREFIX}/bin/
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@${INSTALL_PROGRAM} ${WRKSRC}/misc/454/sff2scf ${PREFIX}/bin/
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.for f in ${BINARIES}
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@${CHMOD} a-r ${PREFIX}/bin/${f}
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.endfor
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.for f in ${CONTRIBS}
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@${INSTALL_SCRIPT} ${WRKSRC}/contributions/${f} ${PREFIX}/bin/
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.endfor
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.for f in ${SCRIPTS}
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@${INSTALL_SCRIPT} ${WRKSRC}/scripts/${f} ${PREFIX}/bin/
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.endfor
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@${MKDIR} ${DATADIR}
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.for f in ${DATAFILES}
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@${INSTALL_DATA} ${WRKSRC}/misc/${f} ${DATADIR}/${f}.dist
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.endfor
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.for f in ${NULLFILES}
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@${INSTALL_DATA} /dev/null ${DATADIR}/${f}.dist
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.endfor
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.if ${PORT_OPTIONS:MEXAMPLES}
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@${MKDIR} ${EXAMPLESDIR}
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.for dir in ${EXAMPLES}
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@${CP} -R ${WRKSRC}/${dir} ${EXAMPLESDIR}
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.endfor
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.endif
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.if ${PORT_OPTIONS:MDOCS}
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@${MKDIR} ${DOCSDIR}
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.for f in ${PORTDOCS}
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@${INSTALL_DATA} ${WRKSRC}/${f} ${DOCSDIR}
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.endfor
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.endif
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.if ! ${PORT_OPTIONS:MEXAMPLES}
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@${ECHO_CMD} "Examples were not installed. You can define WITH_EXAMPLES=yes to install them."
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.endif
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@${ECHO_CMD} "You must set the CONSED_HOME environment variable to '${PREFIX}'"
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.include <bsd.port.mk>
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