biology/paml: update to version 4.9c and various improvements

- Update to version 4.9c
- Set LICENSE=GPLv3
- Use the variable PORTDOCS to automate the generation of the DOCS plist (as
  suggested by mat@).
- Install dat/ examples/ and Technical/ directories as well as files in the root
  directory of the distribution tarball.
- Fix broken permissions.
- Delete Windows executables.
- Build and install useful binaries not built by upstream's Makefile.
- Update pkg-descr.

Reviewed by:	swills (mentor)
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D8040

1 files changed, 37 insertions, 9 deletions

diff --git a/biology/paml/Makefile b/biology/paml/Makefile
index 9a74d5ac1235..265e61490a39 100644
--- a/biology/paml/Makefile
+++ b/biology/paml/Makefile
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	paml
-PORTVERSION=	4.9a
+PORTVERSION=	4.9c
 CATEGORIES=	biology
 MASTER_SITES=	http://abacus.gene.ucl.ac.uk/software/
 DISTNAME=	${PORTNAME}${PORTVERSION}
@@ -10,24 +10,52 @@ DISTNAME=	${PORTNAME}${PORTVERSION}
 MAINTAINER=	jrm@FreeBSD.org
 COMMENT=	Phylogenetic Analysis by Maximum Likelihood (PAML)
 
+LICENSE=	GPLv3
+
 USES=		gmake tar:tgz
-WRKSRC=		${WRKDIR}/${DISTNAME}/src
-MAKE_ARGS=	CC="${CC}" CFLAGS="${CFLAGS}"
 
-BINARIES=	baseml basemlg chi2 codeml evolver pamp yn00
-DOC_FILES=	pamlDOC.pdf pamlFAQs.pdf pamlHistory.txt
+BINARIES=	baseml basemlg chi2 codeml evolver evolverNSbranches \
+		evolverNSbranchsites evolverNSsites pamp yn00
+
+PORTDOCS=	MCMCtree.Tutorials.pdf MCMCtreeDOC.pdf pamlDOC.pdf pamlFAQs.pdf \
+		pamlHistory.txt README.txt
+
+DATA=		3s.trees 4s.trees 5s.trees 6s.trees GeneticCode.txt MCaa.dat	\
+		MCbase.dat MCbaseRandomTree.dat MCcodon.dat aaml.ctl baseml.ctl	\
+		brown.nuc brown.rooted.trees brown.trees codeml.ctl codonml.ctl	\
+		mcmctree.ctl pamp.ctl paupblock paupend paupstart stewart.aa	\
+		stewart.trees yn00.ctl
+PORTDATA=	${DATA} dat examples Technical
 
 OPTIONS_DEFINE=	DOCS
 
+# Fix broken permissions and remove Windows executables
+post-extract:
+	@${CHMOD} -R a+rX ${WRKDIR}
+	@${FIND} ${WRKSRC}/Technical -name "*.exe" -delete
+
+do-build:
+	@cd ${WRKSRC}/src && \
+	${SETENV} ${MAKE_ENV} ${MAKE_CMD}
+.for f in NSbranches NSsites NSbranchsites
+	@cd ${WRKSRC}/src && \
+	${CC} ${CFLAGS} -DCodon${f} -o evolver${f} evolver.c tools.c -lm
+.endfor
+
 do-install:
 .for f in ${BINARIES}
-	${INSTALL_PROGRAM} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/src/${f} ${STAGEDIR}${PREFIX}/bin
+.endfor
+	@${MKDIR} ${STAGEDIR}${DATADIR}
+.for f in ${DATA}
+	${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}/${DATADIR}
 .endfor
+	(cd ${WRKSRC} && ${COPYTREE_SHARE} "dat examples Technical" \
+	${STAGEDIR}/${DATADIR})
 
 do-install-DOCS-on:
 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
-.for f in ${DOC_FILES}
-	${INSTALL_DATA} ${WRKSRC}/../doc/${f} ${STAGEDIR}${DOCSDIR}
-.endfor
+	${INSTALL_DATA} ${WRKSRC}/doc/* ${STAGEDIR}${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/README.txt ${STAGEDIR}${DOCSDIR}
 
 .include <bsd.port.mk>