- Update to version 2.3
PR: ports/116019 Submitted by: KATO Tsuguru
This commit is contained in:
Ion-Mihai Tetcu
parent
ee6a3c0911
commit
68b24c81a3
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=198681
@ -6,7 +6,7 @@
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#
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PORTNAME= migrate
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PORTVERSION= 2.1.3
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PORTVERSION= 2.3
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CATEGORIES= biology
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MASTER_SITES= http://popgen.csit.fsu.edu/currentversion/
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DISTNAME= ${PORTNAME}-${PORTVERSION}.src
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@ -15,41 +15,51 @@ MAINTAINER= ports@FreeBSD.org
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COMMENT= A program to estimate population sizes and migration rates
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WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/src
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USE_GNOME= gnometarget
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GNU_CONFIGURE= yes
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CONFIGURE_TARGET= --build=${MACHINE_ARCH}-portbld-freebsd${OSREL}
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MAKE_ARGS= CFLAGS="${CFLAGS}"
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MAKE_ARGS= HARDWARECFLAGS="${CFLAGS}" \
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MYCPPFLAGS="${CFLAGS} -DNOJPEG -DNOPNG -DNOZLIB"
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MAN1= migrate.1
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MLINKS= migrate.1 migrate-n.1
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DOCS= HISTORY HOWTO-PARALLEL README migrate.html
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EXAMPLES= README infile.ep infile.msat infile.seq \
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outfile-bayes-saved outfile-ml-saved \
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parmfile parmfile.testbayes parmfile.testml
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post-patch:
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@${REINPLACE_CMD} 's,-falign-loops=16,,g' ${WRKSRC}/configure
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do-install:
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@ ${INSTALL_PROGRAM} ${WRKSRC}/migrate-n ${PREFIX}/bin
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@ cd ${PREFIX}/bin && ${LN} -s migrate-n migrate
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@ ${INSTALL_MAN} ${WRKSRC}/migrate.1 ${MAN1PREFIX}/man/man1
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.if !defined(NOPORTDOCS)
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@ ${MKDIR} ${DOCSDIR}/graphics
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.for i in ${DOCS}
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@ ${INSTALL_DATA} ${WRKSRC}/../${i} ${DOCSDIR}
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.endfor
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@ ${MKDIR} ${EXAMPLESDIR}
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.for i in ${EXAMPLES}
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@ ${INSTALL_DATA} ${WRKSRC}/../example/${i} ${EXAMPLESDIR}
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.endfor
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@ ${INSTALL_DATA} ${WRKSRC}/../graphics/* ${DOCSDIR}/graphics
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.endif
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.include <bsd.port.pre.mk>
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.if ${ARCH} == "alpha"
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BROKEN= Does not compile
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NOT_FOR_ARCHS= alpha
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ONLY_FOR_ARCHS_REASON= Does not compile
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.if defined(WITH_THREAD_PRETTY)
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ALL_TARGET= thread-pretty
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.elif defined(WITH_PRETTY)
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ALL_TARGET= pretty
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.elif defined(WITH_THREAD)
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ALL_TARGET= thread
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.else
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ALL_TARGET= all
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.endif
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post-patch:
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@${REINPLACE_CMD} -e \
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's|-lpthread|${PTHREAD_LIBS}|g' ${WRKSRC}/configure
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@${REINPLACE_CMD} -e 's|@CFLAGS@||g ; \
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s|make -f|$$(MAKE) -f|g' ${WRKSRC}/Makefile.in
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do-install:
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${INSTALL_PROGRAM} ${WRKSRC}/migrate-n ${PREFIX}/bin
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${LN} -sf migrate-n ${PREFIX}/bin/migrate
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${INSTALL_MAN} ${WRKSRC}/migrate.1 ${MAN1PREFIX}/man/man1
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.if !defined(NOPORTDOCS)
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@${MKDIR} ${DOCSDIR}
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.for i in HISTORY HOWTO-PARALLEL README migrate.html
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${INSTALL_DATA} ${WRKSRC}/../${i} ${DOCSDIR}
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.endfor
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@${MKDIR} ${DOCSDIR}/graphics
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${INSTALL_DATA} ${WRKSRC}/../graphics/* ${DOCSDIR}/graphics
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.endif
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.if !defined(NOPORTEXAMPLES)
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@${MKDIR} ${EXAMPLESDIR}
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${INSTALL_DATA} ${WRKSRC}/../example/* ${EXAMPLESDIR}
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.endif
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.include <bsd.port.post.mk>
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@ -1,3 +1,3 @@
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MD5 (migrate-2.1.3.src.tar.gz) = fdff82f3dd509811fa4780287a554931
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SHA256 (migrate-2.1.3.src.tar.gz) = 91c8636c5b7a189fd693ddb9a863ff5995abf7157f10bf005e8e3e2497d56023
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SIZE (migrate-2.1.3.src.tar.gz) = 1637715
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MD5 (migrate-2.3.src.tar.gz) = 12dbf7bd9d69b6ba87a9ba16b68ff7e5
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SHA256 (migrate-2.3.src.tar.gz) = 3407a92b41f23d036a6ef5fd11f77e6d1aa8ee39fa4f61c65b0f71670b8b8f62
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SIZE (migrate-2.3.src.tar.gz) = 1952466
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@ -3,12 +3,5 @@ two or "n" populations assuming a migration matrix model with asymmetric
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migration rates and different subpopulation sizes. The n-population migrate
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can use sequence data, microsatellite data or electrophoretic data.
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Migrate forms part of the Lamarc (Likelihood Analysis with Metropolis
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Algorithm using Random Coalescence) suite. See:
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http://evolution.genetics.washington.edu/lamarc.html
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Author: Peter Beerli <beerli@genetics.washington.edu>
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WWW: http://evolution.genetics.washington.edu/lamarc/migrate.html
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-- Johann Visagie <wjv@FreeBSD.org>
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Author: Peter Beerli <beerli@scs.fsu.edu>
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WWW: http://popgen.scs.fsu.edu/Migrate-n.html
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@ -8,15 +8,23 @@ bin/migrate-n
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%%PORTDOCS%%%%DOCSDIR%%/graphics/migrate.gif
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%%PORTDOCS%%%%DOCSDIR%%/graphics/packet.gif
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%%PORTDOCS%%%%DOCSDIR%%/migrate.html
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%%PORTDOCS%%%%EXAMPLESDIR%%/README
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%%PORTDOCS%%%%EXAMPLESDIR%%/infile.ep
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%%PORTDOCS%%%%EXAMPLESDIR%%/infile.msat
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%%PORTDOCS%%%%EXAMPLESDIR%%/infile.seq
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%%PORTDOCS%%%%EXAMPLESDIR%%/outfile-bayes-saved
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%%PORTDOCS%%%%EXAMPLESDIR%%/outfile-ml-saved
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%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile
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%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.testbayes
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%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.testml
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%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bayesfile
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.benchmark
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.ep
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.msat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.seq
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-saved
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-saved
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.pdf
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.benchmark
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.ep
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.msat
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.seq
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testbayes
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testml
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%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
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%%PORTDOCS%%@dirrm %%DOCSDIR%%/graphics
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%%PORTDOCS%%@dirrm %%DOCSDIR%%
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