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Index: head/biology/paml/Makefile
===================================================================
--- head/biology/paml/Makefile
+++ head/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 @@
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>
Index: head/biology/paml/distinfo
===================================================================
--- head/biology/paml/distinfo
+++ head/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
Index: head/biology/paml/pkg-descr
===================================================================
--- head/biology/paml/pkg-descr
+++ head/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
Index: head/biology/paml/pkg-plist
===================================================================
--- head/biology/paml/pkg-plist
+++ head/biology/paml/pkg-plist
@@ -3,8 +3,8 @@
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

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