academic/PhyTime: Added (Phylogenetic estimation).

Signed-off-by: David Spencer <idlemoor@slackbuilds.org>

academic/PhyTime/PhyTime.SlackBuild

@@ -0,0 +1,113 @@
+#!/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}

academic/PhyTime/PhyTime.info

@@ -0,0 +1,10 @@
+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"

academic/PhyTime/README

@@ -0,0 +1,2 @@
+PhyTime is a PhyML - related software, that estimates maximum likelihood
+phylogenies from alignments of nucleotide or amino acid sequences.

academic/PhyTime/References

@@ -0,0 +1,8 @@
+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.

academic/PhyTime/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------------------------------------------------------|
+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: