5 files changed, 40 insertions, 88 deletions

diff --git a/biology/migrate/Makefile b/biology/migrate/Makefile
index 18457f50637d..a407b2d9ec16 100644
--- a/biology/migrate/Makefile
+++ b/biology/migrate/Makefile
@@ -6,9 +6,9 @@
 #
 
 PORTNAME=	migrate
-PORTVERSION=	3.0.3
+PORTVERSION=	3.1.1
 CATEGORIES=	biology
-MASTER_SITES=	http://people.scs.fsu.edu/~beerli/popgen/currentversion/
+MASTER_SITES=	http://people.sc.fsu.edu/~beerli/popgen/currentversion/
 DISTNAME=	${PORTNAME}-${PORTVERSION}.src
 
 MAINTAINER=	ports@FreeBSD.org
@@ -20,8 +20,11 @@ GNU_CONFIGURE=	yes
 CONFIGURE_ENV=	ac_cv_prog_GMAKE="${MAKE}"
 MAKE_ARGS=	PRETTYCFLAGS="${CFLAGS} -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY"
 
-MAN1=		migrate.1
-MLINKS=		migrate.1 migrate-n.1
+MAN1=		${PORTNAME}.1
+MLINKS=		${PORTNAME}.1 ${PORTNAME}-n.1
+PORTDOCS=	*
+PORTEXAMPLES=	*
+PLIST_FILES=	bin/${PORTNAME} bin/${PORTNAME}-n
 
 .include <bsd.port.pre.mk>
 
@@ -41,14 +44,16 @@ ALL_TARGET=	all
 post-patch:
 	@${REINPLACE_CMD} -e 's|="-O "|="$$CFLAGS"|g ; \
 		 s|-lpthread|${PTHREAD_LIBS}|g' ${WRKSRC}/configure
+	@${REINPLACE_CMD} -e '/PRETTY$$/d' ${WRKSRC}/definitions.h
+	@${REINPLACE_CMD} -e 's|-O3||g' ${WRKSRC}/haru/makefile.gcc
 
 do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/migrate-n ${PREFIX}/bin
-	${LN} -sf migrate-n ${PREFIX}/bin/migrate
-	${INSTALL_MAN} ${WRKSRC}/migrate.1 ${MAN1PREFIX}/man/man1
+	${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME}-n ${PREFIX}/bin
+	${LN} -sf ${PORTNAME}-n ${PREFIX}/bin/${PORTNAME}
+	${INSTALL_MAN} ${WRKSRC}/${PORTNAME}.1 ${MAN1PREFIX}/man/man1
 .if !defined(NOPORTDOCS)
 	@${MKDIR} ${DOCSDIR}
-.for i in HISTORY HOWTO-PARALLEL README migrate.html
+.for i in HISTORY HOWTO-PARALLEL README ${PORTNAME}.html
 	${INSTALL_DATA} ${WRKSRC}/../${i} ${DOCSDIR}
 .endfor
 	@${MKDIR} ${DOCSDIR}/graphics
diff --git a/biology/migrate/distinfo b/biology/migrate/distinfo
index df9ec6b2ae18..044e499eee62 100644
--- a/biology/migrate/distinfo
+++ b/biology/migrate/distinfo
@@ -1,3 +1,3 @@
-MD5 (migrate-3.0.3.src.tar.gz) = ea4a67a6320300a4df554f74a272581e
-SHA256 (migrate-3.0.3.src.tar.gz) = d00c1999e7af055aca9f30565dfb610b03e42c2dcc60838c9c4367be87d0edd1
-SIZE (migrate-3.0.3.src.tar.gz) = 5660159
+MD5 (migrate-3.1.1.src.tar.gz) = 5870d5e980a4bb9b34e4ea50d86ef98a
+SHA256 (migrate-3.1.1.src.tar.gz) = 2149dadb91b164aea77759b4757aa8cc6269fc50743664bef05dc32239a9ad58
+SIZE (migrate-3.1.1.src.tar.gz) = 3874625
diff --git a/biology/migrate/files/patch-main.c b/biology/migrate/files/patch-main.c
new file mode 100644
index 000000000000..2cb9bcf9e3fc
--- /dev/null
+++ b/biology/migrate/files/patch-main.c
@@ -0,0 +1,23 @@
+--- main.c.orig	2010-01-20 23:47:41.000000000 +0900
++++ main.c	2010-02-01 23:02:52.000000000 +0900
+@@ -630,7 +630,9 @@
+ 	      {
+ 		fprintf(EARTH->outfile,"%5li %10.5f\n",locus+1,universe[locus]->averageheat);
+ 	      }
++#ifdef PRETTY
+ 	    pdf_print_averageheat(universe,options);
++#endif
+ 	  }
+ #ifdef PRETTY
+ 	pdf_print_end_time(&page_height);
+@@ -2443,8 +2445,10 @@
+     {
+       fprintf(file,"\n\nLocus      Raw Thermodynamic score(1a)  Bezier approximated score(1b)     Harmonic mean(2)\n");
+       fprintf(file,"------------------------------------------------------------------------------------------\n");
++#ifdef PRETTY
+       if(file==EARTH->outfile)
+ 	pdf_bayes_factor_rawscores_header(EARTH,options);
++#endif
+     }
+   if(options->heating)//-----------------------heating
+     {
diff --git a/biology/migrate/pkg-descr b/biology/migrate/pkg-descr
index aa5a24629a0a..3aaa0693067c 100644
--- a/biology/migrate/pkg-descr
+++ b/biology/migrate/pkg-descr
@@ -3,4 +3,4 @@ two or "n" populations assuming a migration matrix model with asymmetric
 migration rates and different subpopulation sizes.  The n-population migrate
 can use sequence data, microsatellite data or electrophoretic data.
 
-WWW:    http://popgen.csit.fsu.edu/Migrate-n.html
+WWW:    http://popgen.sc.fsu.edu/Migrate-n.html
diff --git a/biology/migrate/pkg-plist b/biology/migrate/pkg-plist
deleted file mode 100644
index bccdc40fe777..000000000000
--- a/biology/migrate/pkg-plist
+++ /dev/null
@@ -1,76 +0,0 @@
-bin/migrate
-bin/migrate-n
-%%PORTDOCS%%%%DOCSDIR%%/HISTORY
-%%PORTDOCS%%%%DOCSDIR%%/HOWTO-PARALLEL
-%%PORTDOCS%%%%DOCSDIR%%/README
-%%PORTDOCS%%%%DOCSDIR%%/graphics/librarian.gif
-%%PORTDOCS%%%%DOCSDIR%%/graphics/mail.gif
-%%PORTDOCS%%%%DOCSDIR%%/graphics/migrate.gif
-%%PORTDOCS%%%%DOCSDIR%%/graphics/packet.gif
-%%PORTDOCS%%%%DOCSDIR%%/migrate.html
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/aicfile
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bayesallfile
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bayesallfile.dated
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bayesfile
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bayesfile.dated
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/datefile.dated
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.benchmark
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.dated
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.ep
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.msat
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.seq
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mighistfile.dated
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-1
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-2
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-brown
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-multi0.5
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-multi0.5-0.5
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-saved
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-step
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-dated.pdf
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-3
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-3.pdf
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-paral2
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-saved
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-single
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-watkins-0.5-0.5
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml.pdf
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.benchmark
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.benchmark_double
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.benchmark_float
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.dated
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.pdf
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outifle-ml-3
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile-testbayes.txt
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.benchmark
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.dated
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.ep
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.gugus
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.msat
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.seq
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testbayes
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testml
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testml-save
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pretty
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/skylinefile.dated
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile-1
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile-2
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile-3
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile-mpi-ml
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile-single
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sumfile1
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/treefile
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/treefile-1
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/treefile-2
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/treefile-3
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/treefile.dated
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/graphics
-%%PORTDOCS%%@dirrm %%DOCSDIR%%