diff options
| -rw-r--r-- | academic/PhyML/PhyML.SlackBuild | 33 | ||||
| -rw-r--r-- | academic/PhyML/PhyML.info | 8 | ||||
| -rw-r--r-- | academic/PhyML/References | 2 | ||||
| -rw-r--r-- | academic/PhyML/slack-desc | 10 |
4 files changed, 32 insertions, 21 deletions
diff --git a/academic/PhyML/PhyML.SlackBuild b/academic/PhyML/PhyML.SlackBuild index 05fb80d8cc..08ee51b623 100644 --- a/academic/PhyML/PhyML.SlackBuild +++ b/academic/PhyML/PhyML.SlackBuild @@ -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! - -# 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. +# 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. + +# 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-$VERSION/References diff --git a/academic/PhyML/PhyML.info b/academic/PhyML/PhyML.info index 9eb0f43c06..334dc43132 100644 --- a/academic/PhyML/PhyML.info +++ b/academic/PhyML/PhyML.info @@ -1,10 +1,10 @@ PRGNAM="PhyML" -VERSION="20110526" +VERSION="20110919" HOMEPAGE="http://code.google.com/p/phyml/" -DOWNLOAD="http://phyml.googlecode.com/files/phyml-20110526.tar.gz" -MD5SUM="04e707ee6e0bda6259e75ab82a87e818" +DOWNLOAD="http://phyml.googlecode.com/files/phyml-20110919.tar.gz" +MD5SUM="d95c73c5c03d082db21564a54978f281" DOWNLOAD_x86_64="" MD5SUM_x86_64="" MAINTAINER="Petar Petrov" EMAIL="ppetrov@paju.oulu.fi" -APPROVED="Niels Horn" +APPROVED="rworkman" diff --git a/academic/PhyML/References b/academic/PhyML/References index 0d69b95fe4..17fd35add2 100644 --- a/academic/PhyML/References +++ b/academic/PhyML/References @@ -1,5 +1,3 @@ -References - New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0. Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. Systematic Biology, diff --git a/academic/PhyML/slack-desc b/academic/PhyML/slack-desc index a4ddd88a6a..be2d634abf 100644 --- a/academic/PhyML/slack-desc +++ b/academic/PhyML/slack-desc @@ -6,14 +6,14 @@ # customary to leave one space after the ':'. |-----handy-ruler------------------------------------------------------| -PhyML: PhyML (Phylogeny software) +PhyML: PhyML (Phylogenetic estimation using Maximum Likelihood) PhyML: PhyML: PhyML is a software that estimates maximum likelihood phylogenies -PhyML: from alignments of nucleotide or amino acid sequences. It provides a -PhyML: wide range of options that were designed to facilitate standard +PhyML: from alignments of nucleotide or amino acid sequences. It provides +PhyML: a wide range of options that were designed to facilitate standard PhyML: phylogenetic analyses. PhyML: -PhyML: -PhyML: PhyML: References: /usr/doc/PhyML-$VERSION/References PhyML: Home: http://code.google.com/p/phyml/ +PhyML: +PhyML: |