diff options
author | Petar Petrov <ppetrov@paju.oulu.fi> | 2013-01-13 11:16:51 +0100 |
---|---|---|
committer | dsomero <xgizzmo@slackbuilds.org> | 2013-01-20 09:03:02 -0500 |
commit | 906fb4874df40c307db9e8d7227af05e102f8a16 (patch) | |
tree | 52476baa80f6382ad18d3dd825d71355456c9baa /academic/mrbayes | |
parent | 191857cec786b4ff66e46f5c9aa7821acbe9dc92 (diff) |
academic/mrbayes: Added (Bayesian Inference of Phylogeny).
Signed-off-by: Matteo Bernardini <ponce@slackbuilds.org>
Diffstat (limited to 'academic/mrbayes')
-rw-r--r-- | academic/mrbayes/README | 9 | ||||
-rw-r--r-- | academic/mrbayes/References | 9 | ||||
-rw-r--r-- | academic/mrbayes/mrbayes.SlackBuild | 104 | ||||
-rw-r--r-- | academic/mrbayes/mrbayes.info | 10 | ||||
-rw-r--r-- | academic/mrbayes/slack-desc | 19 |
5 files changed, 151 insertions, 0 deletions
diff --git a/academic/mrbayes/README b/academic/mrbayes/README new file mode 100644 index 0000000000000..4787afa0d5816 --- /dev/null +++ b/academic/mrbayes/README @@ -0,0 +1,9 @@ +MrBayes: Bayesian Inference of Phylogeny + +MrBayes is a program for Bayesian inference and model choice across a +wide range of phylogenetic and evolutionary models. MrBayes uses +Markov chain Monte Carlo (MCMC) methods to estimate the posterior +distribution of model parameters. + +For citing information, check the program's web site, the pdf manual +and the References file in /usr/doc/mrbayes-*. diff --git a/academic/mrbayes/References b/academic/mrbayes/References new file mode 100644 index 0000000000000..dab69ad94db0a --- /dev/null +++ b/academic/mrbayes/References @@ -0,0 +1,9 @@ +Excerp from the Manual_MrBayes_v3.2.0_draft.pdf + +1.8 Citing the Program +If you wish to cite the program, you can simply refer to the most +recent release note (Ronquist et al., 2011). This manual should be +cited as an online publication. For more tips on citations, you can +run the citations command in the program, which will give you a +number of other relevant citations for the program and its models +and algorithms. diff --git a/academic/mrbayes/mrbayes.SlackBuild b/academic/mrbayes/mrbayes.SlackBuild new file mode 100644 index 0000000000000..b0b8fd12a3d0b --- /dev/null +++ b/academic/mrbayes/mrbayes.SlackBuild @@ -0,0 +1,104 @@ +#!/bin/sh + +# Slackware build script for mrbayes + +# Copyright 2013 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. + +PRGNAM=mrbayes +VERSION=${VERSION:-3.2.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i486 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i486" ]; then + SLKCFLAGS="-O2 -march=i486 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf ${PRGNAM}_${VERSION} +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd ${PRGNAM}_${VERSION} +chown -R root:root . +find . \ + \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ + -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ + -exec chmod 644 {} \; + +cd src +autoconf + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --with-beagle=no \ + --build=$ARCH-slackware-linux + +make +install -D -m755 mb $PKG/usr/bin/$PRGNAM + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + gpl.txt ../documentation/* \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/mrbayes/mrbayes.info b/academic/mrbayes/mrbayes.info new file mode 100644 index 0000000000000..6344a430152f9 --- /dev/null +++ b/academic/mrbayes/mrbayes.info @@ -0,0 +1,10 @@ +PRGNAM="mrbayes" +VERSION="3.2.1" +HOMEPAGE="http://mrbayes.sourceforge.net/" +DOWNLOAD="http://downloads.sourceforge.net/mrbayes/mrbayes-3.2.1.tar.gz" +MD5SUM="477c9f39126db360f92c5b6a7c9cca95" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" diff --git a/academic/mrbayes/slack-desc b/academic/mrbayes/slack-desc new file mode 100644 index 0000000000000..df8f35aaf00e5 --- /dev/null +++ b/academic/mrbayes/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +mrbayes: mrbayes (MrBayes: Bayesian Inference of Phylogeny) +mrbayes: +mrbayes: MrBayes is a program for Bayesian inference and model choice +mrbayes: across a wide range of phylogenetic and evolutionary models. +mrbayes: MrBayes uses Markov chain Monte Carlo (MCMC) methods to +mrbayes: estimate the posterior distribution of model parameters. +mrbayes: +mrbayes: Home: http://mrbayes.sourceforge.net/ +mrbayes: References: /usr/doc/mrbayes-$VERSION/References +mrbayes: +mrbayes: |