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1ca81797c4
PR: ports/157527 Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> Approved by: bapt (mentor)
93 lines
2.6 KiB
Makefile
93 lines
2.6 KiB
Makefile
# New ports collection makefile for: velvet
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# Date created: 27 Oct 2009
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# Whom: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
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#
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# $FreeBSD$
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#
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PORTNAME= velvet
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PORTVERSION= 1.1.04
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CATEGORIES= biology
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MASTER_SITES= http://www.ebi.ac.uk/~zerbino/velvet/
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DISTNAME= ${PORTNAME}_${PORTVERSION}
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EXTRACT_SUFX= .tgz
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MAINTAINER= mzaki@m.u-tokyo.ac.jp
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COMMENT= Sequence assembler for very short reads
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USE_GMAKE= yes
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ALL_TARGET= default
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MAXKMERLENGTH?= 31
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VELVET_CATEGORIES?= 2
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MAKE_ENV+= MAXKMERLENGTH=${MAXKMERLENGTH} CATEGORIES=${VELVET_CATEGORIES}
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USE_PERL5_RUN= yes
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BINARIES= velvetg velveth
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SCRIPTS= shuffleSequences_fasta.pl shuffleSequences_fastq.pl \
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contrib/VelvetOptimiser-2.1.7/VelvetOptimiser.pl \
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contrib/afg_handling/asmbly_splitter.pl \
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contrib/afg_handling/snp_view.pl \
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contrib/columbus_scripts/enlarge_exons.pl \
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contrib/columbus_scripts/gff2fasta.pl \
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contrib/columbus_scripts/merge_gtf_exons.pl \
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contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl \
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contrib/extractContigReads/extractContigReads.pl \
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contrib/fasta2agp/fasta2agp.pl \
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contrib/observed-insert-length.pl/observed-insert-length.pl \
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contrib/select_paired/select_paired.pl \
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contrib/show_repeats/show_repeats.pl
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PERLMOD_DIRS= contrib/VelvetOptimiser-2.1.7/VelvetOpt
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PERLMOD_FILES= contrib/VelvetOptimiser-2.1.7/VelvetOpt/Assembly.pm \
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contrib/VelvetOptimiser-2.1.7/VelvetOpt/Utils.pm \
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contrib/VelvetOptimiser-2.1.7/VelvetOpt/gwrap.pm \
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contrib/VelvetOptimiser-2.1.7/VelvetOpt/hwrap.pm
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.if !defined(WITHOUT_PYTHON)
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USE_PYTHON= yes
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SCRIPTS+= contrib/AssemblyAssembler1.3/AssemblyAssembler1.3.py
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.endif
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.for f in ${BINARIES} ${SCRIPTS}
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PLIST_FILES+= bin/${f:T}
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.endfor
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.for d in ${PERLMOD_DIRS}
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PLIST_DIRS+= %%SITE_PERL%%/${d:T}
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.endfor
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.for f in ${PERLMOD_FILES}
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PLIST_FILES+= %%SITE_PERL%%/${f:H:T}/${f:T}
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.endfor
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PORTDOCS= ChangeLog Manual.pdf Columbus_manual.pdf
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post-patch:
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.for f in ${SCRIPTS}
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${REINPLACE_CMD} -e s,#!/usr/bin/perl,${PERL}, ${WRKSRC}/${f}
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.endfor
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.if !defined(WITHOUT_PYTHON)
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${REINPLACE_CMD} -e s,#!/usr/bin/python,${PYTHON_CMD}, ${WRKSRC}/contrib/AssemblyAssembler1.3/AssemblyAssembler1.3.py
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.endif
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do-install:
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.for f in ${BINARIES}
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${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin
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.endfor
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.for f in ${SCRIPTS}
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${INSTALL_SCRIPT} ${WRKSRC}/${f} ${PREFIX}/bin/${f:T}
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.endfor
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.for d in ${PERLMOD_DIRS}
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${MKDIR} ${PREFIX}/${SITE_PERL_REL}/${d:T}
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.endfor
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.for f in ${PERLMOD_FILES}
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${INSTALL_DATA} ${WRKSRC}/${f} ${PREFIX}/${SITE_PERL_REL}/${f:H:T}/${f:T}
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.endfor
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.if !defined(NOPORTDOCS)
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${MKDIR} ${DOCSDIR}
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.for f in ${PORTDOCS}
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${INSTALL_MAN} ${WRKSRC}/${f} ${DOCSDIR}
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.endfor
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.endif
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.include <bsd.port.mk>
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