Convert biology to MDOCS and MEXAMPLES

14 files changed, 46 insertions, 20 deletions

diff --git a/biology/biojava/Makefile b/biology/biojava/Makefile
index 3115443baa3b..8dbc541f2a58 100644
--- a/biology/biojava/Makefile
+++ b/biology/biojava/Makefile
@@ -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 && \
diff --git a/biology/blast/Makefile b/biology/blast/Makefile
index 81bef22fa5b7..1d7729e02de1 100644
--- a/biology/blast/Makefile
+++ b/biology/blast/Makefile
@@ -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}
diff --git a/biology/consed/Makefile b/biology/consed/Makefile
index 93979f541942..7176663aa5a3 100644
--- a/biology/consed/Makefile
+++ b/biology/consed/Makefile
@@ -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}'"
diff --git a/biology/finchtv/Makefile b/biology/finchtv/Makefile
index f0fbf6bb57bc..8baa30643700 100644
--- a/biology/finchtv/Makefile
+++ b/biology/finchtv/Makefile
@@ -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 ${DOCSDIR}
diff --git a/biology/mafft/Makefile b/biology/mafft/Makefile
index 95c9055ff890..8ef06d99f0d4 100644
--- a/biology/mafft/Makefile
+++ b/biology/mafft/Makefile
@@ -65,7 +65,7 @@ do-install:
 .endfor
 	@${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}
diff --git a/biology/mummer/Makefile b/biology/mummer/Makefile
index 6879eb0929ec..210dd0c2deab 100644
--- a/biology/mummer/Makefile
+++ b/biology/mummer/Makefile
@@ -20,6 +20,9 @@ SCRIPTS=	dnadiff exact-tandems mapview mummerplot nucmer \
 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})
diff --git a/biology/njplot/Makefile b/biology/njplot/Makefile
index b1452be06fb8..5bd019723a73 100644
--- a/biology/njplot/Makefile
+++ b/biology/njplot/Makefile
@@ -31,6 +31,8 @@ PORTDOCS=	njplot.help njplot.html njplot.gif
 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}
diff --git a/biology/p5-bioperl-run/Makefile b/biology/p5-bioperl-run/Makefile
index 2227b8cbde04..0bdebb18cd5a 100644
--- a/biology/p5-bioperl-run/Makefile
+++ b/biology/p5-bioperl-run/Makefile
@@ -129,10 +129,13 @@ MAN3=	Bio::Tools::Run::Phylo::Phylip::DrawGram.3 \
 
 # 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}
diff --git a/biology/p5-bioperl/Makefile b/biology/p5-bioperl/Makefile
index e48e04b7d8f2..fe7cd4ca83b5 100644
--- a/biology/p5-bioperl/Makefile
+++ b/biology/p5-bioperl/Makefile
@@ -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}
diff --git a/biology/paml/Makefile b/biology/paml/Makefile
index 5f982ec42193..354246c42fe5 100644
--- a/biology/paml/Makefile
+++ b/biology/paml/Makefile
@@ -18,11 +18,14 @@ BINARIES=	baseml basemlg chi2 codeml evolver pamp yn00
 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}
diff --git a/biology/phd2fasta/Makefile b/biology/phd2fasta/Makefile
index 1301596f0719..617c2dcbcad8 100644
--- a/biology/phd2fasta/Makefile
+++ b/biology/phd2fasta/Makefile
@@ -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}
diff --git a/biology/phrap/Makefile b/biology/phrap/Makefile
index adb56a79cb9e..7fc22cae6b16 100644
--- a/biology/phrap/Makefile
+++ b/biology/phrap/Makefile
@@ -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}
diff --git a/biology/phred/Makefile b/biology/phred/Makefile
index 99ab3f200deb..d185d91dcbd2 100644
--- a/biology/phred/Makefile
+++ b/biology/phred/Makefile
@@ -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} ${DOCSDIR}
diff --git a/biology/velvet/Makefile b/biology/velvet/Makefile
index 5287ed1022da..6f8929b208fc 100644
--- a/biology/velvet/Makefile
+++ b/biology/velvet/Makefile
@@ -59,6 +59,9 @@ PLIST_FILES+=	%%SITE_PERL%%/${f:H:T}/${f:T}
 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}