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academic/PhyML: Updated for version 20110919.

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Signed-off-by: Robby Workman <rworkman@slackbuilds.org>
This commit is contained in:
Petar Petrov 2011-12-20 00:19:37 -06:00 committed by Robby Workman
parent 5baa0033cd
commit f3eaf0c230
4 changed files with 31 additions and 20 deletions
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31
academic/PhyML/PhyML.SlackBuild
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@ -1,18 +1,31 @@
#!/bin/sh
# Slackware build script for PhyML
# Written by Petar Petrov, <ppetrov@paju.oulu.fi> and
# hereby submitted to the public domain
# Thanks to Niels Horn for the handy modifications and
# corrections!
# Copyright 2011 Petar Petrov, ppetrov@paju.oulu.fi
# All rights reserved.
#
# Redistribution and use of this script, with or without modification, is
# permitted provided that the following conditions are met:
#
# 1. Redistributions of this script must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# THIS SLACKBUILD IS DISTRIBUTETD IN THE HOPE OF BEING
# USEFUL BUT WITHOUT ANY WARRANTY. THE AUTHOR IS _NOT_
# RESPONSIBLE FOR ANY DAMAGE OR DATA LOSS CAUSED BY IT.
# Thanks to Niels Horn for some handy modifications and corrections.
PRGNAM=PhyML
VERSION=${VERSION:-20110526}
VERSION=${VERSION:-20110919}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
@ -83,7 +96,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr
mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
cp -a \
doc/phyml_manual.pdf AUTHORS ChangeLog COPYING INSTALL README \
doc/$SRCNAM-manual-$VERSION.pdf AUTHORS ChangeLog COPYING INSTALL README \
$PKG/usr/doc/$PRGNAM-$VERSION
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References

8
academic/PhyML/PhyML.info
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@ -1,10 +1,10 @@
PRGNAM="PhyML"
VERSION="20110526"
VERSION="20110919"
HOMEPAGE="http://code.google.com/p/phyml/"
DOWNLOAD="http://phyml.googlecode.com/files/phyml-20110526.tar.gz"
MD5SUM="04e707ee6e0bda6259e75ab82a87e818"
DOWNLOAD="http://phyml.googlecode.com/files/phyml-20110919.tar.gz"
MD5SUM="d95c73c5c03d082db21564a54978f281"
DOWNLOAD_x86_64=""
MD5SUM_x86_64=""
MAINTAINER="Petar Petrov"
EMAIL="ppetrov@paju.oulu.fi"
APPROVED="Niels Horn"
APPROVED="rworkman"

2
academic/PhyML/References
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@ -1,5 +1,3 @@
References
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies:
Assessing the Performance of PhyML 3.0. Guindon S., Dufayard J.F.,
Lefort V., Anisimova M., Hordijk W., Gascuel O. Systematic Biology,

10
academic/PhyML/slack-desc
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@ -6,14 +6,14 @@
# customary to leave one space after the ':'.
|-----handy-ruler------------------------------------------------------|
PhyML: PhyML (Phylogeny software)
PhyML: PhyML (Phylogenetic estimation using Maximum Likelihood)
PhyML:
PhyML: PhyML is a software that estimates maximum likelihood phylogenies
PhyML: from alignments of nucleotide or amino acid sequences. It provides a
PhyML: wide range of options that were designed to facilitate standard
PhyML: from alignments of nucleotide or amino acid sequences. It provides
PhyML: a wide range of options that were designed to facilitate standard
PhyML: phylogenetic analyses.
PhyML:
PhyML:
PhyML:
PhyML: References: /usr/doc/PhyML-$VERSION/References
PhyML: Home: http://code.google.com/p/phyml/
PhyML:
PhyML: