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mirror of https://git.FreeBSD.org/ports.git synced 2024-12-12 03:00:28 +00:00

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
This commit is contained in:
Joseph Mingrone 2016-09-28 02:30:29 +00:00
parent 29a8954d58
commit 512daaacda
Notes: svn2git 2021-03-31 03:12:20 +00:00
svn path=/head/; revision=422846
4 changed files with 49 additions and 34 deletions

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@ -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)
USES= gmake tar:tgz
WRKSRC= ${WRKDIR}/${DISTNAME}/src
MAKE_ARGS= CC="${CC}" CFLAGS="${CFLAGS}"
LICENSE= GPLv3
BINARIES= baseml basemlg chi2 codeml evolver pamp yn00
DOC_FILES= pamlDOC.pdf pamlFAQs.pdf pamlHistory.txt
USES= gmake tar:tgz
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>

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@ -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

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@ -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

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@ -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