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# New ports collection makefile for: wise |
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# Created by: Tony Maher <tonym@biolateral.com.au> |
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# Date created: 26 February 2002 |
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# Whom: Tony Maher <tonym@biolateral.com.au> |
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# |
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# $FreeBSD: head/biology/wise/Makefile 300895 2012-07-14 12:56:14Z beat $ |
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# $FreeBSD: head/biology/wise/Makefile 300895 2012-07-14 12:56:14Z beat $ |
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# |
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PORTNAME= wise |
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PORTNAME= wise |
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PORTVERSION= 2.2.0 |
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PORTVERSION= 2.4.1 |
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CATEGORIES= biology |
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CATEGORIES= biology |
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MASTER_SITES= ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/ |
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MASTER_SITES= http://www.ebi.ac.uk/~birney/wise2/ |
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DISTNAME= ${PORTNAME}${PORTVERSION} |
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DISTNAME= ${PORTNAME}${PORTVERSION} |
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MAINTAINER= ports@FreeBSD.org |
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MAINTAINER= ports@FreeBSD.org |
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COMMENT= Intelligent algorithms for DNA searches |
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COMMENT= Intelligent algorithms for DNA searches |
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WRKTOP= ${WRKDIR}/${DISTNAME} |
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OPTIONS_DEFINE= DOCS EXAMPLES |
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WRKSRC= ${WRKTOP}/src |
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BUILD_WRKSRC= ${WRKSRC}/src |
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USE_GNOME= glib20 |
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MAKEFILE= makefile |
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MAKEFILE= makefile |
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MAKE_JOBS_SAFE= yes |
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SUB_FILES= pkg-message |
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SUB_FILES= pkg-message |
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PORTDOCS= * |
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PORTEXAMPLES= * |
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PLIST_FILES= ${BINFILES:S,^,bin/,} ${DATAFILES:S,^,%%DATADIR%%/,} |
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PLIST_DIRS= %%DATADIR%% |
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# |
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# Actually want an 'ALL_TARGET = all perl' which then requires |
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# Actually want an 'ALL_TARGET = all perl' which then requires |
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# 'USE_PERL5= yes' but the perl sub-build is currently broken. |
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# 'USE_PERL5= yes' but the perl sub-build is currently broken. |
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# something like '@cd ${WRKSRC}/perl/Wise2; ${MAKE} install' |
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# something like '@cd ${WRKSRC}/perl/Wise2; ${MAKE} install' |
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# |
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BINFILES= dba dnal estwise estwisedb genewise genewisedb \ |
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BINFILES= dba dnal estwise estwisedb genewise genewisedb promoterwise \ |
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genomewise psw pswdb |
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psw pswdb scanwise scanwise_server |
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DATAFILES= BLOSUM30.bla BLOSUM45.bla BLOSUM62.bla BLOSUM80.bla \ |
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DATAFILES= BLOSUM30.bla BLOSUM45.bla BLOSUM62.bla BLOSUM80.bla aa.rnd \ |
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aa.rnd blosum30.bla blosum62.bla cb.tmf codon.table \ |
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cb.tmf codon.table gene.stat gon120.bla gon160.bla \ |
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gene.stat gon120.bla gon160.bla gon200.bla gon250.bla \ |
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gon200.bla gon250.bla gon350.bla human.gf human.gp \ |
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gon350.bla human.gf human.gp human.stats idenity.bla \ |
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human.stats idenity.bla methods pb.gf pombe.gf tm.pri \ |
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methods pb.gf pombe.gf tm.pri wise.2 wise.per worm.gf |
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wise.2 wise.per worm.gf |
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DOCFILES= README apiend.tex appendix.tex dynamite.tex \ |
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genewise21.eps genewise6.eps gettex.pl makefile \ |
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.include <bsd.port.options.mk> |
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wise2.tex wise2api.tex wise3arch.tex |
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EXFILES= README db.hmm hn_est.fa human.genomic \ |
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post-patch: |
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keratin_intron.human keratin_intron.mouse pep.fa \ |
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@${FIND} ${BUILD_WRKSRC} -name "makefile" | ${XARGS} \ |
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road.pep rrm.HMM vav.dna xeno.cdna xeno.pep |
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${REINPLACE_CMD} -e \ |
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's|^CC =|CC ?=| ; \ |
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# |
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s|^CFLAGS =|CFLAGS +=| ; \ |
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# Top level makefile does not respect CFLAGS. Fixing it means |
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s|-O[0-9] | | ; \ |
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# having to fix some of the sub-directory makefiles. |
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s|-g | | ; \ |
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# Note: some makefiles are ok and know that '-c' does not belong |
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s|-g[0-9] | | ; \ |
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# in CFLAGS and are part of the rule. |
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s|-lpthread|-pthread| ; \ |
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# |
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s|glib-config|pkg-config glib-2.0| ; \ |
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/welcome.csh/s|^|#|' |
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post-configure: |
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@${REINPLACE_CMD} \ |
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-e s'#^CFLAGS = -c -O#CFLAGS ?= -c -O#;' \ |
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-e s'#\tcsh welcome.csh##;' \ |
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${WRKSRC}/${MAKEFILE} |
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@${REINPLACE_CMD} \ |
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-e s'#CFLAGS) $?#CFLAGS) -c $?#;' \ |
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${WRKSRC}/base/${MAKEFILE} |
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@${REINPLACE_CMD} \ |
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-e s'#INCFLAGS) $?#INCFLAGS) -c $?#;' \ |
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${WRKSRC}/dynlibsrc/${MAKEFILE} |
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@${REINPLACE_CMD} \ |
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-e s'#INCFLAGS) $?#INCFLAGS) -c $?#;' \ |
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-e s'#CFLAGS) estwise.c#CFLAGS) -c estwise.c#;' \ |
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-e s'#CFLAGS) estwiseb.c#CFLAGS) -c estwiseb.c#;' \ |
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-e s'#CFLAGS) estwisedb.c#CFLAGS) -c estwisedb.c#;' \ |
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-e s'#CFLAGS) genewise.c#CFLAGS) -c genewise.c#;' \ |
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-e s'#CFLAGS) genewisedb.c#CFLAGS) -c genewisedb.c#;' \ |
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${WRKSRC}/models/${MAKEFILE} |
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do-install: |
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do-install: |
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.for file in ${BINFILES} |
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.for i in ${BINFILES} |
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@${INSTALL_PROGRAM} ${WRKSRC}/bin/${file} ${PREFIX}/bin |
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(cd ${BUILD_WRKSRC}/bin && ${INSTALL_PROGRAM} ${i} ${PREFIX}/bin) |
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.endfor |
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.endfor |
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@${MKDIR} ${DATADIR} |
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@${MKDIR} ${DATADIR} |
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.for file in ${DATAFILES} |
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.for i in ${DATAFILES} |
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@${INSTALL_DATA} ${WRKTOP}/wisecfg/${file} ${DATADIR} |
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(cd ${WRKSRC}/wisecfg && ${INSTALL_DATA} ${i} ${DATADIR}) |
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.endfor |
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.endfor |
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.if !defined(NOPORTDOCS) |
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.if ${PORT_OPTIONS:MDOCS} |
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@${MKDIR} ${DOCSDIR} |
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@${MKDIR} ${DOCSDIR} |
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.for file in ${DOCFILES} |
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@(cd ${WRKSRC}/docs && ${COPYTREE_SHARE} . ${DOCSDIR}) |
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@${INSTALL_DATA} ${WRKTOP}/docs/${file} ${DOCSDIR} |
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.endif |
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.endfor |
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.if ${PORT_OPTIONS:MEXAMPLES} |
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@${MKDIR} ${EXAMPLESDIR} |
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@${MKDIR} ${EXAMPLESDIR} |
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.for file in ${EXFILES} |
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@(cd ${WRKSRC}/test_data && ${COPYTREE_SHARE} . ${EXAMPLESDIR}) |
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@${INSTALL_DATA} ${WRKTOP}/test_data/${file} ${EXAMPLESDIR} |
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.endfor |
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.endif |
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.endif |
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post-install: |
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@${CAT} ${PKGMESSAGE} |
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@${CAT} ${PKGMESSAGE} |
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.include <bsd.port.mk> |
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.include <bsd.port.mk> |