academic/PhyTime: Added (Phylogenetic estimation).

Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
This commit is contained in:
Petar Petrov 2016-11-26 20:44:53 +00:00 committed by Willy Sudiarto Raharjo
parent 6be5245485
commit bcc8330bee
No known key found for this signature in database
GPG key ID: 887B8374D7333381
6 changed files with 1743 additions and 0 deletions

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#!/bin/sh
# Slackware build script for PhyTime
# Copyright 2016 Petar Petrov slackalaxy@gmail.com
# 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=PhyTime
VERSION=${VERSION:-20131112}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
SRCNAM=phyml
SRCVER=20120412
if [ -z "$ARCH" ]; then
case "$( uname -m )" in
i?86) ARCH=i586 ;;
arm*) ARCH=arm ;;
*) ARCH=$( uname -m ) ;;
esac
fi
CWD=$(pwd)
TMP=${TMP:-/tmp/SBo}
PKG=$TMP/package-$PRGNAM
OUTPUT=${OUTPUT:-/tmp}
if [ "$ARCH" = "i586" ]; then
SLKCFLAGS="-O2 -march=i586 -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 $SRCNAM-$SRCVER
tar xvf $CWD/${SRCNAM}_${SRCVER}.orig.tar.gz
cd $SRCNAM-$SRCVER
chown -R root:root .
find -L . \
\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
-o -perm 511 \) -exec chmod 755 {} \; -o \
\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
# Apply version patch
cd src
patch -i $CWD/$VERSION.patch
cd ..
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--enable-phytime \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION \
--build=$ARCH-slackware-linux
# Use our CFLAGS
sed -i "/^CFLAGS/s/=/+=/" src/Makefile
sed -i "/^CFLAGS/s/=/+=/" Makefile
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$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 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
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}

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PRGNAM="PhyTime"
VERSION="20131112"
HOMEPAGE="https://github.com/stephaneguindon/phyml/"
DOWNLOAD="http://http.debian.net/debian/pool/main/p/phyml/phyml_20120412.orig.tar.gz"
MD5SUM="d2207a3d6caf633c43239a01ce70f244"
DOWNLOAD_x86_64=""
MD5SUM_x86_64=""
REQUIRES=""
MAINTAINER="Petar Petrov"
EMAIL="slackalaxy@gmail.com"

2
academic/PhyTime/README Normal file
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PhyTime is a PhyML - related software, that estimates maximum likelihood
phylogenies from alignments of nucleotide or amino acid sequences.

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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.
Bayesian estimation of divergence times from large sequence alignments.
Mol Biol Evol. 2010 Aug;27(8):1768-81. doi: 10.1093/molbev/msq060.
Epub 2010 Mar 1.

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# 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------------------------------------------------------|
PhyTime: PhyTime (Phylogenetic estimation using Maximum Likelihood)
PhyTime:
PhyTime: PhyTime estimates maximum likelihood phylogenies from alignments
PhyTime: of nucleotide or amino acid sequences.
PhyTime:
PhyTime:
PhyTime:
PhyTime:
PhyTime:
PhyTime:
PhyTime: