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

4 files changed, 48 insertions, 33 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>
diff --git a/biology/paml/distinfo b/biology/paml/distinfo
index 00a59125bc88..7165f2139526 100644
--- a/biology/paml/distinfo
+++ b/biology/paml/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1463365805
-SHA256 (paml4.9a.tgz) = 1400b6a48aa7ba2dee637352430a1f64594674168cf7a749ac79093da9a39ef4
-SIZE (paml4.9a.tgz) = 5853303
+TIMESTAMP = 1474920596
+SHA256 (paml4.9c.tgz) = c0c5fb1e1af5a27b2bd80c9daaa91c259157f34a44d297e058f1b9d8689dce02
+SIZE (paml4.9c.tgz) = 5405921
diff --git a/biology/paml/pkg-descr b/biology/paml/pkg-descr
index 142aea337cd7..68733fd977c8 100644
--- a/biology/paml/pkg-descr
+++ b/biology/paml/pkg-descr
@@ -1,22 +1,9 @@
 Phylogenetic Analysis by Maximum Likelihood (PAML)
 
-PAML is a program package for phylogenetic analyses of DNA or protein
-sequences using maximum likelihood, and is maintained and distributed
-by Ziheng Yang.
-
-Possible uses of the programs are:
-- Estimation of branch lengths in a phylogenetic tree and parameters
-  in the evolutionary model such as the transition/transversion rate
-  ratio, the shape parameter of the gamma distribution for variable
-  evolutionary rates among sites, and rate parameters for different
-  genes;
-- Test of hypotheses concerning sequence evolution, such as rate
-  constancy and independence among nucleotide or amino acid sites, rate
-  constancy among lineages (the molecular clock), and homogeneity of
-  evolutionary process in multiple genes;
-- Calculation of substitution rates at sites;
-- Reconstruction of ancestral nucleotide or amino acid sequences;
-- Simulation of nucleotide, codon, and amino acid sequence data sets;
-- Phylogenetic tree reconstruction by maximum likelihood and Bayesian methods.
+PAML is a package of programs for phylogenetic analyses of DNA or protein
+sequences using maximum likelihood.  It is not good for tree making.  It may be
+used to estimate parameters and test hypotheses for the study the evolutionary
+process using trees reconstructed with programs such as PAUP*, PHYLIP, MOLPHY,
+PhyML, or RaxML.
 
 WWW: http://abacus.gene.ucl.ac.uk/software/paml.html
diff --git a/biology/paml/pkg-plist b/biology/paml/pkg-plist
index a7eb37b020f2..3755a5660cbb 100644
--- a/biology/paml/pkg-plist
+++ b/biology/paml/pkg-plist
@@ -3,8 +3,8 @@ bin/basemlg
 bin/chi2
 bin/codeml
 bin/evolver
+bin/evolverNSbranches
+bin/evolverNSbranchsites
+bin/evolverNSsites
 bin/pamp
 bin/yn00
-%%PORTDOCS%%%%DOCSDIR%%/pamlDOC.pdf
-%%PORTDOCS%%%%DOCSDIR%%/pamlFAQs.pdf
-%%PORTDOCS%%%%DOCSDIR%%/pamlHistory.txt