82a87de90c
Mk/Uses/linux.mk.
- Replace USE_LINUX=yes with USES+=linux and USE_LINUX=(.*) with
USES+=linux:\1 in all ports.
- Replace USE_LINUX_APPS with USE_LINUX in all ports.
- Use INSTALL_SCRIPT instead of INSTALL_PROGRAM to install scripts in some
ports.
- When USE_LINUX_RPM is defined, simplify the way DISTFILES and EXTRACT_ONLY
are defined.
- Remove BRANDELF_DIRS and BRANDELF_FILES handling. In the very rare cases
that it is still necessary ports can run ${BRANDELF} from post-patch.
- Remove AUTOMATIC_PLIST handling. Only one port used it.
- Fix Linux MASTER_SITES.
- Replace OVERRIDE_LINUX_BASE_PORT and OVERRIDE_LINUX_NONBASE_PORTS with
default versions framework.
- bsd.port.mk:
- Move Linux related bits to Uses/linux.mk, except USE_LINUX_PREFIX.
- Put USE_LINUX_PREFIX handling after USES processing.
- Define DOCSDIR, DATADIR, etc. after handling USE_LINUX_PREFIX so it can
give these variables a different default value.
- When a package needs to run Linux ldconfig check before installation if
Linux support is enabled.
- emulators/linux_base-*:
- Use USES=linux and remove duplication.
- Remove files/lp. FreeBSD or CUPS lp(1) should work.
- Remove files/yp.conf. No longer seems to be used.
- Remove pkg-deinstall and move pkg-install into pkg-plist.
- Update pkg-descr and pkg-message.
- Fix handling of ldconfig cache in pkg-plist.
- devel/fb-adb: Use a Linux shell to run a Linux script but patch the script
to use FreeBSD mkdir so mkdir -p $path creates $path and not
/compat/linux/$path.
PR: 211645
Exp-run by: antoine
Approved by: portmgr (antoine)
82 lines
2.3 KiB
Makefile
82 lines
2.3 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= 27.0
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CATEGORIES= biology
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# MASTER_SITES= http://www.phrap.org/consed/distributions/${PORTVERSION}/
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# MASTER_SITES= http://bozeman.mbt.washington.edu/consed/distributions/${PORTVERSION}/
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DISTNAME= ${PORTNAME}_linux
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MAINTAINER= mzaki@m.u-tokyo.ac.jp
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COMMENT= Graphical tool for editing Phrap assemblies
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RUN_DEPENDS= phred:biology/phred \
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phrap:biology/phrap
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CONFLICTS_INSTALL= phd2fasta-[0-9]*
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SUB_FILES= pkg-message
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USES= linux perl5 shebangfix
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USE_LINUX= xorglibs
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ONLY_FOR_ARCHS= i386 amd64
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MYSHEBANG= bin/ace2Fasta.perl \
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bin/tagRepeats.perl \
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bin/selectRegions.perl \
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bin/selectOneRegion.perl \
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bin/revertToUneditedRead \
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bin/removeReads \
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bin/phredPhrap.orig \
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bin/phredPhrap \
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bin/phd2Ace.perl \
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bin/orderPrimerPairs.perl \
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bin/makeRegionsFile.perl \
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bin/makePhdBall.perl \
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bin/lib2Phd.perl \
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bin/fixContigEnd.perl \
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bin/findSequenceMatchesForConsed.perl \
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bin/revert_fof \
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bin/filter454Reads.perl \
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bin/fastq2Phrap.perl \
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bin/fasta2PhdBall.perl \
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bin/fasta2Phd.perl \
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bin/fasta2Ace.perl \
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bin/determineReadTypes.perl \
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bin/countEditedBases.perl \
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bin/bam2Ace.perl \
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bin/amplifyTranscripts.perl \
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bin/alignSolexaReads2Refs.perl \
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bin/alignRNA2Genomic.perl \
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bin/addSolexaReads.perl \
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bin/addSangerReads.perl \
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bin/addReads2Consed.perl \
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bin/add454Reads.perl \
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bin/ace2Oligos.perl \
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bin/transferConsensusTags.perl \
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bin/ace2fof \
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bin/ace2OligosWithComments.perl \
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bin/sff2phd.perl \
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bin/recover_consensus_tags \
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bin/phredPhrapWithPhdBalls \
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bin/cons.perl \
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bin/acestatus.pl \
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bin/aceContigs2Phds.perl \
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bin/sff2phd_Samborskyy
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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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NO_BUILD= yes
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do-install:
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${MKDIR} ${STAGEDIR}${DATADIR}
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${LN} -sf ../../bin ${STAGEDIR}${DATADIR}/bin
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(cd ${WRKSRC}; ${SETENV} CC=${CC} ./installConsed.perl consed_linux32bit ${STAGEDIR}${DATADIR})
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${LN} -sf ../../../etc/PhredPar/phredpar.dat ${STAGEDIR}${DATADIR}/lib/phredpar.dat
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cd ${STAGEDIR}${PREFIX} && ${ECHO_CMD} ${MYSHEBANG} | ${XARGS} ${SED} -i '' ${_SHEBANG_REINPLACE_ARGS}
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.include <bsd.port.mk>
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