Date: Fri, 3 Jan 2014 15:46:52 +0000 (UTC) From: Adam Weinberger <adamw@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r338550 - in head/biology: biojava blast consed finchtv mafft mummer njplot p5-bioperl p5-bioperl-run paml phd2fasta phrap phred velvet Message-ID: <201401031546.s03FkqRx020433@svn.freebsd.org>
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Author: adamw Date: Fri Jan 3 15:46:52 2014 New Revision: 338550 URL: http://svnweb.freebsd.org/changeset/ports/338550 Log: Convert biology to MDOCS and MEXAMPLES Modified: head/biology/biojava/Makefile head/biology/blast/Makefile head/biology/consed/Makefile head/biology/finchtv/Makefile head/biology/mafft/Makefile head/biology/mummer/Makefile head/biology/njplot/Makefile head/biology/p5-bioperl-run/Makefile head/biology/p5-bioperl/Makefile head/biology/paml/Makefile head/biology/phd2fasta/Makefile head/biology/phrap/Makefile head/biology/phred/Makefile head/biology/velvet/Makefile Modified: head/biology/biojava/Makefile ============================================================================== --- head/biology/biojava/Makefile Fri Jan 3 15:36:03 2014 (r338549) +++ head/biology/biojava/Makefile Fri Jan 3 15:46:52 2014 (r338550) @@ -24,8 +24,11 @@ PORTDOCS= biojava PORTEXAMPLES= demos WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION} -.if !defined(WITHOUT_TESTS) NO_STAGE= yes + +.include <bsd.port.options.mk> + +.if !defined(WITHOUT_TESTS) regression-test: @(cd ${BUILD_WRKSRC}; \ ${SETENV} ${MAKE_ENV} ${ANT} ${MAKE_ARGS} runtests) @@ -40,7 +43,7 @@ do-install: .endfor @${ECHO_MSG} " [ DONE ]" -.if !defined(NOPORTDOCS) +.if ${PORT_OPTIONS:MDOCS} @${ECHO_MSG} -n ">> Installing documentation in ${DOCSDIR}..." @${MKDIR} ${DOCSDIR} @${INSTALL_DATA} ${WRKSRC}/LICENSE ${DOCSDIR} @@ -51,7 +54,7 @@ do-install: @${ECHO_MSG} " [ DONE ]" .endif -.if !defined(NOPORTEXAMPLES) +.if ${PORT_OPTIONS:MEXAMPLES} @${ECHO_MSG} -n ">> Installing examples in ${EXAMPLESDIR}..." @${MKDIR} ${EXAMPLESDIR} cd ${WRKSRC}/doc && \ Modified: head/biology/blast/Makefile ============================================================================== --- head/biology/blast/Makefile Fri Jan 3 15:36:03 2014 (r338549) +++ head/biology/blast/Makefile Fri Jan 3 15:46:52 2014 (r338550) @@ -59,7 +59,7 @@ do-install: .for xlink in ${XDFORMAT_LINKS} @(cd ${PREFIX}/bin && ${LN} -s xdformat ${xlink}) .endfor -.if !defined (NOPORTDOCS) +.if ${PORT_OPTIONS:MDOCS} @${MKDIR} ${DOCSDIR} .for doc in ${PORTDOCS} ${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR} Modified: head/biology/consed/Makefile ============================================================================== --- head/biology/consed/Makefile Fri Jan 3 15:36:03 2014 (r338549) +++ head/biology/consed/Makefile Fri Jan 3 15:46:52 2014 (r338550) @@ -53,12 +53,15 @@ PORTDATA+= ${f}.dist .endfor PORTDOCS= README.txt -.if defined(WITH_EXAMPLES) +NO_STAGE= yes + +.include <bsd.port.options.mk> + +.if ${PORT_OPTIONS:MEXAMPLES} EXAMPLES= standard autofinish assembly_view polyphred PLIST= ${PKGDIR}/pkg-plist.examples .endif -NO_STAGE= yes post-build: (cd ${WRKSRC}/misc/454; ${CC} ${CFLAGS} sffinfo.c -o sffinfo) (cd ${WRKSRC}/misc/454; ${CC} ${CFLAGS} sff2scf.c -o sff2scf) @@ -84,19 +87,19 @@ do-install: .for f in ${NULLFILES} @${INSTALL_DATA} /dev/null ${DATADIR}/${f}.dist .endfor -.if !defined(NOPORTEXAMPLES) +.if ${PORT_OPTIONS:MEXAMPLES} @${MKDIR} ${EXAMPLESDIR} .for dir in ${EXAMPLES} @${CP} -R ${WRKSRC}/${dir} ${EXAMPLESDIR} .endfor .endif -.if !defined(NOPORTDOCS) +.if ${PORT_OPTIONS:MDOCS} @${MKDIR} ${DOCSDIR} .for f in ${PORTDOCS} @${INSTALL_DATA} ${WRKSRC}/${f} ${DOCSDIR} .endfor .endif -.if !defined(WITH_EXAMPLES) +.if ! ${PORT_OPTIONS:MEXAMPLES} @${ECHO_CMD} "Examples were not installed. You can define WITH_EXAMPLES=yes to install them." .endif @${ECHO_CMD} "You must set the CONSED_HOME environment variable to '${PREFIX}'" Modified: head/biology/finchtv/Makefile ============================================================================== --- head/biology/finchtv/Makefile Fri Jan 3 15:36:03 2014 (r338549) +++ head/biology/finchtv/Makefile Fri Jan 3 15:46:52 2014 (r338550) @@ -19,8 +19,11 @@ SUB_FILES= pkg-message STRIP= NO_STAGE= yes + +.include <bsd.port.options.mk> + do-install: -.if !defined(NOPORTDOCS) +.if ${PORT_OPTIONS:MDOCS} @${MKDIR} ${DOCSDIR} ${INSTALL_DATA} ${WRKSRC}/License.txt ${DOCSDIR} ${INSTALL_DATA} ${WRKSRC}/ReleaseNotes.txt ${DOCSDIR} Modified: head/biology/mafft/Makefile ============================================================================== --- head/biology/mafft/Makefile Fri Jan 3 15:36:03 2014 (r338549) +++ head/biology/mafft/Makefile Fri Jan 3 15:46:52 2014 (r338550) @@ -65,7 +65,7 @@ do-install: .endfor @${MKDIR} ${EXAMPLESDIR} ${INSTALL_DATA} ${WRKSRC}/test/* ${EXAMPLESDIR} -.if !defined(NOPORTDOCS) +.if ${PORT_OPTIONS:MDOCS} @${MKDIR} ${DOCSDIR} ${INSTALL_DATA} ${WRKSRC}/readme ${DOCSDIR} ${INSTALL_DATA} ${WRKSRC}/license ${DOCSDIR} Modified: head/biology/mummer/Makefile ============================================================================== --- head/biology/mummer/Makefile Fri Jan 3 15:36:03 2014 (r338549) +++ head/biology/mummer/Makefile Fri Jan 3 15:46:52 2014 (r338550) @@ -20,6 +20,9 @@ SCRIPTS= dnadiff exact-tandems mapview m DOCUMENTS= COPYRIGHT INSTALL LICENSE README NO_STAGE= yes + +.include <bsd.port.options.mk> + do-install: .for program in ${PROGRAMS} (cd ${WRKSRC} && ${INSTALL_PROGRAM} ${program} ${PREFIX}/bin) @@ -29,7 +32,7 @@ do-install: (cd ${WRKSRC} && ${INSTALL_SCRIPT} ${script} ${PREFIX}/bin) .endfor -.if !defined(NOPORTDOCS) +.if ${PORT_OPTIONS:MDOCS} @${MKDIR} ${DOCSDIR} .for doc in ${DOCUMENTS} (cd ${WRKSRC} && ${INSTALL_DATA} ${doc} ${DOCSDIR}) Modified: head/biology/njplot/Makefile ============================================================================== --- head/biology/njplot/Makefile Fri Jan 3 15:36:03 2014 (r338549) +++ head/biology/njplot/Makefile Fri Jan 3 15:46:52 2014 (r338550) @@ -31,6 +31,8 @@ PORTDOCS= njplot.help njplot.html njplot MAN1= njplot.1 unrooted.1 NO_STAGE= yes +.include <bsd.port.options.mk> + .ifdef (WITHOUT_X11) post-patch: ${REINPLACE_CMD} -e 's|njplot.*unrooted||' ${WRKSRC}/makefile @@ -43,7 +45,7 @@ do-install: .for file in ${MAN1} ${INSTALL_MAN} ${WRKSRC}/${file} ${PREFIX}/man/man1 .endfor -.if !defined(NOPORTDOCS) +.if ${PORT_OPTIONS:MDOCS} ${MKDIR} ${DOCSDIR} .for file in ${PORTDOCS} ${INSTALL_MAN} ${WRKSRC}/${file} ${DOCSDIR} Modified: head/biology/p5-bioperl-run/Makefile ============================================================================== --- head/biology/p5-bioperl-run/Makefile Fri Jan 3 15:36:03 2014 (r338549) +++ head/biology/p5-bioperl-run/Makefile Fri Jan 3 15:46:52 2014 (r338550) @@ -129,10 +129,13 @@ MAN3= Bio::Tools::Run::Phylo::Phylip::Dr # now install all extra stuff (docs, examples, scripts) NO_STAGE= yes + +.include <bsd.port.options.mk> + post-install: ${MKDIR} ${DATADIR} @${CP} -Rv ${WRKSRC}/scripts ${DATADIR} -.if !defined(NOPORTDOCS) +.if ${PORT_OPTIONS:MDOCS} ${MKDIR} ${DOCSDIR} .for doc in AUTHORS Changes INSTALL.PROGRAMS README ${INSTALL_DATA} ${WRKSRC}/${doc} ${DOCSDIR} Modified: head/biology/p5-bioperl/Makefile ============================================================================== --- head/biology/p5-bioperl/Makefile Fri Jan 3 15:36:03 2014 (r338549) +++ head/biology/p5-bioperl/Makefile Fri Jan 3 15:46:52 2014 (r338550) @@ -984,12 +984,15 @@ MAN3= Bio::Align::AlignI.3 \ # now install all extra stuff (docs, examples, scripts, models) NO_STAGE= yes + +.include <bsd.port.options.mk> + post-install: ${MKDIR} ${DATADIR} ${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${DATADIR} ${MKDIR} ${EXAMPLESDIR} ${CP} -R ${WRKSRC}/examples/* ${EXAMPLESDIR} -.if !defined(NOPORTDOCS) +.if ${PORT_OPTIONS:MDOCS} ${MKDIR} ${DOCSDIR} .for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE MANIFEST README ${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR} Modified: head/biology/paml/Makefile ============================================================================== --- head/biology/paml/Makefile Fri Jan 3 15:36:03 2014 (r338549) +++ head/biology/paml/Makefile Fri Jan 3 15:46:52 2014 (r338550) @@ -18,11 +18,14 @@ BINARIES= baseml basemlg chi2 codeml evo DOC_FILES= MCMCtreeDoc.pdf pamlDOC.pdf pamlFAQs.pdf pamlHistory.txt NO_STAGE= yes + +.include <bsd.port.options.mk> + do-install: .for f in ${BINARIES} ${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin .endfor -.if !defined(NOPORTDOCS) +.if ${PORT_OPTIONS:MDOCS} ${MKDIR} ${DOCSDIR} .for f in ${DOC_FILES} ${INSTALL_DATA} ${WRKDIR}/${PORTNAME}44/doc/${f} ${DOCSDIR} Modified: head/biology/phd2fasta/Makefile ============================================================================== --- head/biology/phd2fasta/Makefile Fri Jan 3 15:36:03 2014 (r338549) +++ head/biology/phd2fasta/Makefile Fri Jan 3 15:46:52 2014 (r338550) @@ -38,7 +38,7 @@ do-install: .for f in ${BINARIES} @${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin/ .endfor -.if !defined(NOPORTDOCS) +.if ${PORT_OPTIONS:MDOCS} @${MKDIR} ${DOCSDIR} .for f in ${PORTDOCS} @${INSTALL_DATA} ${WRKSRC}/${f} ${DOCSDIR} Modified: head/biology/phrap/Makefile ============================================================================== --- head/biology/phrap/Makefile Fri Jan 3 15:36:03 2014 (r338549) +++ head/biology/phrap/Makefile Fri Jan 3 15:46:52 2014 (r338550) @@ -52,7 +52,7 @@ do-install: .for f in ${PORTDATA} @${INSTALL_DATA} ${WRKSRC}/${f} ${DATADIR} .endfor -.if !defined(NOPORTDOCS) +.if ${PORT_OPTIONS:MDOCS} @${MKDIR} ${DOCSDIR} .for f in ${PORTDOCS} @${INSTALL_DATA} ${WRKSRC}/${f} ${DOCSDIR} Modified: head/biology/phred/Makefile ============================================================================== --- head/biology/phred/Makefile Fri Jan 3 15:36:03 2014 (r338549) +++ head/biology/phred/Makefile Fri Jan 3 15:46:52 2014 (r338550) @@ -51,7 +51,7 @@ do-install: .for f in ${DATAFILES} @${INSTALL_DATA} ${WRKSRC}/${f} ${DATADIR}/${f}.dist .endfor -.if !defined(NOPORTDOCS) +.if ${PORT_OPTIONS:MDOCS} @${MKDIR} ${DOCSDIR} .for f in ${PORTDOCS} @${INSTALL_DATA} ${WRKSRC}/${f} ${DOCSDIR} Modified: head/biology/velvet/Makefile ============================================================================== --- head/biology/velvet/Makefile Fri Jan 3 15:36:03 2014 (r338549) +++ head/biology/velvet/Makefile Fri Jan 3 15:46:52 2014 (r338550) @@ -59,6 +59,9 @@ PLIST_FILES+= %%SITE_PERL%%/${f:H:T}/${f PORTDOCS= ChangeLog Manual.pdf Columbus_manual.pdf NO_STAGE= yes + +.include <bsd.port.options.mk> + post-patch: .for f in ${SCRIPTS} ${REINPLACE_CMD} -e s,#!/usr/bin/perl,${PERL}, ${WRKSRC}/${f} @@ -80,7 +83,7 @@ do-install: .for f in ${PERLMOD_FILES} ${INSTALL_DATA} ${WRKSRC}/${f} ${PREFIX}/${SITE_PERL_REL}/${f:H:T}/${f:T} .endfor -.if !defined(NOPORTDOCS) +.if ${PORT_OPTIONS:MDOCS} ${MKDIR} ${DOCSDIR} .for f in ${PORTDOCS} ${INSTALL_MAN} ${WRKSRC}/${f} ${DOCSDIR}
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