diff options
| -rw-r--r-- | academic/PhyML/PhyML.SlackBuild | 94 | ||||
| -rw-r--r-- | academic/PhyML/PhyML.info | 10 | ||||
| -rw-r--r-- | academic/PhyML/README | 10 | ||||
| -rw-r--r-- | academic/PhyML/References | 6 | ||||
| -rw-r--r-- | academic/PhyML/slack-desc | 19 |
5 files changed, 139 insertions, 0 deletions
diff --git a/academic/PhyML/PhyML.SlackBuild b/academic/PhyML/PhyML.SlackBuild new file mode 100644 index 0000000000000..5fb6ce9fcfbff --- /dev/null +++ b/academic/PhyML/PhyML.SlackBuild @@ -0,0 +1,94 @@ +#!/bin/sh + +# Slackware build script for PhyML +# Written by Petar Petrov, <ppetrov@paju.oulu.fi> and +# hereby submitted to the public domain + +# 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. + +PRGNAM=PhyML +VERSION=${VERSION:-3.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=$(echo $PRGNAM | tr A-Z a-z) +SRCVER=2010023 + +if [ -z "$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 $SRCNAM +tar xvf $CWD/${SRCNAM}_$SRCVER.tar.gz +cd $SRCNAM +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 {} \; + +aclocal +autoconf -f +automake -f +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux + +#Use our CFLAGS +sed -i "/^AM_CFLAGS/s/=/+=/" src/Makefile + +AM_CFLAGS="$SLKCFLAGS" \ + make +make install DESTDIR=$PKG + +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 \ + AUTHORS ChangeLog COPYING INSTALL \ + $PKG/usr/doc/$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/PhyML/PhyML.info b/academic/PhyML/PhyML.info new file mode 100644 index 0000000000000..8008d1b6ba376 --- /dev/null +++ b/academic/PhyML/PhyML.info @@ -0,0 +1,10 @@ +PRGNAM="PhyML" +VERSION="3.0" +HOMEPAGE="http://www.atgc-montpellier.fr/phyml/" +DOWNLOAD="http://phyml.googlecode.com/files/phyml_2010023.tar.gz" +MD5SUM="80a4e936a17b25ba0175e29d64285b05" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" +APPROVED="Niels Horn" diff --git a/academic/PhyML/README b/academic/PhyML/README new file mode 100644 index 0000000000000..f86217a2ad53e --- /dev/null +++ b/academic/PhyML/README @@ -0,0 +1,10 @@ +PhyML is a phylogeny software based on the maximum-likelihood +principle. Early PhyML versions used a fast algorithm to perform +Nearest Neighbor Interchanges (NNIs), in order to improve a +reasonable starting tree topology. + +For details and citation +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, 59(3):307-21, 2010.
\ No newline at end of file diff --git a/academic/PhyML/References b/academic/PhyML/References new file mode 100644 index 0000000000000..0d69b95fe4dd3 --- /dev/null +++ b/academic/PhyML/References @@ -0,0 +1,6 @@ +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, +59(3):307-21, 2010. diff --git a/academic/PhyML/slack-desc b/academic/PhyML/slack-desc new file mode 100644 index 0000000000000..00859ef7ab834 --- /dev/null +++ b/academic/PhyML/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 ':'. + + |-----handy-ruler------------------------------------------------------| +PhyML: PhyML (Phylogeny software) +PhyML: +PhyML: PhyML is a phylogeny software based on the maximum-likelihood +PhyML: principle. Early PhyML versions used a fast algorithm to perform +PhyML: Nearest Neighbor Interchanges (NNIs), in order to improve a +PhyML: reasonable starting tree topology. +PhyML: +PhyML: +PhyML: +PhyML: References: /usr/doc/PhyML-$VERSION/References +PhyML: Home: http://www.atgc-montpellier.fr/phyml/ |