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# Created by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
# $FreeBSD$
PORTNAME= consed
PORTVERSION= 27.0
CATEGORIES= biology
# MASTER_SITES= http://www.phrap.org/consed/distributions/${PORTVERSION}/
MASTER_SITES= http://bozeman.mbt.washington.edu/consed/distributions/${PORTVERSION}/
DISTNAME= ${PORTNAME}_linux
MAINTAINER= mzaki@m.u-tokyo.ac.jp
COMMENT= Graphical tool for editing Phrap assemblies
BROKEN= Unfetchable
RUN_DEPENDS= phred:${PORTSDIR}/biology/phred \
phrap:${PORTSDIR}/biology/phrap
CONFLICTS_INSTALL= phd2fasta-[0-9]*
SUB_FILES= pkg-message
USES= perl5 shebangfix
USE_LINUX= yes
USE_LINUX_APPS= xorglibs
ONLY_FOR_ARCHS= i386 amd64
MYSHEBANG= bin/ace2Fasta.perl \
bin/tagRepeats.perl \
bin/selectRegions.perl \
bin/selectOneRegion.perl \
bin/revertToUneditedRead \
bin/removeReads \
bin/phredPhrap.orig \
bin/phredPhrap \
bin/phd2Ace.perl \
bin/orderPrimerPairs.perl \
bin/makeRegionsFile.perl \
bin/makePhdBall.perl \
bin/lib2Phd.perl \
bin/fixContigEnd.perl \
bin/findSequenceMatchesForConsed.perl \
bin/revert_fof \
bin/filter454Reads.perl \
bin/fastq2Phrap.perl \
bin/fasta2PhdBall.perl \
bin/fasta2Phd.perl \
bin/fasta2Ace.perl \
bin/determineReadTypes.perl \
bin/countEditedBases.perl \
bin/bam2Ace.perl \
bin/amplifyTranscripts.perl \
bin/alignSolexaReads2Refs.perl \
bin/alignRNA2Genomic.perl \
bin/addSolexaReads.perl \
bin/addSangerReads.perl \
bin/addReads2Consed.perl \
bin/add454Reads.perl \
bin/ace2Oligos.perl \
bin/transferConsensusTags.perl \
bin/ace2fof \
bin/ace2OligosWithComments.perl \
bin/sff2phd.perl \
bin/recover_consensus_tags \
bin/phredPhrapWithPhdBalls \
bin/cons.perl \
bin/acestatus.pl \
bin/aceContigs2Phds.perl \
bin/sff2phd_Samborskyy
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
NO_BUILD= yes
do-install:
${MKDIR} ${STAGEDIR}${DATADIR}
${LN} -sf ../../bin ${STAGEDIR}${DATADIR}/bin
(cd ${WRKSRC}; ${SETENV} CC=${CC} ./installConsed.perl consed_linux32bit ${STAGEDIR}${DATADIR})
${LN} -sf ../../../etc/PhredPar/phredpar.dat ${STAGEDIR}${DATADIR}/lib/phredpar.dat
cd ${STAGEDIR}${PREFIX} && ${ECHO_CMD} ${MYSHEBANG} | ${XARGS} ${SED} -i '' ${_SHEBANG_REINPLACE_ARGS}
.include <bsd.port.mk>
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