From ed2873b79768098aefa030f6dc32f080b73447f4 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Fri, 2 Aug 2019 00:45:41 +0700 Subject: academic/RAxML: Added (Randomized Axelerated Maximum Likelihood). Signed-off-by: Willy Sudiarto Raharjo --- academic/RAxML/RAxML.SlackBuild | 155 ++++++++++++++++++++++++++++++++++++++++ academic/RAxML/RAxML.info | 10 +++ academic/RAxML/README | 16 +++++ academic/RAxML/References | 4 ++ academic/RAxML/slack-desc | 19 +++++ 5 files changed, 204 insertions(+) create mode 100644 academic/RAxML/RAxML.SlackBuild create mode 100644 academic/RAxML/RAxML.info create mode 100644 academic/RAxML/README create mode 100644 academic/RAxML/References create mode 100644 academic/RAxML/slack-desc (limited to 'academic/RAxML') diff --git a/academic/RAxML/RAxML.SlackBuild b/academic/RAxML/RAxML.SlackBuild new file mode 100644 index 0000000000..0c4e98a6ce --- /dev/null +++ b/academic/RAxML/RAxML.SlackBuild @@ -0,0 +1,155 @@ +#!/bin/sh + +# Slackware build script for RAxML + +# Copyright 2019 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=RAxML +VERSION=${VERSION:-8.2.12} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$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 $TMP +rm -rf standard-$PRGNAM-$VERSION +tar xvf $CWD/standard-$PRGNAM-$VERSION.tar.gz +cd standard-$PRGNAM-$VERSION +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 {} \; + +# Build executables with the default Slackware compiler flags. + +# Sequential version +cp Makefile.gcc Makefile +sed -i "/^CFLAGS/s/=/+=/" Makefile +sed -i "s|raxmlHPC|raxml|g" Makefile +CFLAGS="$SLKCFLAGS" \ +make -f Makefile +install -D -m755 raxml $PKG/usr/bin/raxml + +# Openmpi version +cp Makefile.MPI.gcc Makefile.MPI +sed -i "/^CFLAGS/s/=/+=/" Makefile.MPI +sed -i "s|raxmlHPC-MPI|raxml-MPI|g" Makefile.MPI +CFLAGS="$SLKCFLAGS" \ +make -f Makefile.MPI +install -D -m755 raxml-MPI $PKG/usr/bin/raxml-MPI + +########################################################################## +### You are highly encouraged to try the other optimisations below for ### +### performance enhancements. Just uncomment the corresponding lines. ### +########################################################################## + +## Default sequential version +#make -f Makefile.gcc +#install -D -m755 raxmlHPC $PKG/usr/bin/raxmlHPC + +#make -f Makefile.SSE3.gcc +#install -D -m755 raxmlHPC-SSE3 $PKG/usr/bin/raxmlHPC-SSE3 + +#make -f Makefile.AVX.gcc +#install -D -m755 raxmlHPC-AVX $PKG/usr/bin/raxmlHPC-AVX + +## Pthreads version +#make -f Makefile.PTHREADS.gcc +#install -D -m755 raxmlHPC-PTHREADS $PKG/usr/bin/raxmlHPC-PTHREADS + +#make -f Makefile.SSE3.PTHREADS.gcc +#install -D -m755 raxmlHPC-PTHREADS-SSE3 $PKG/usr/bin/raxmlHPC-PTHREADS-SSE3 + +#make -f Makefile.AVX.PTHREADS.gcc +#install -D -m755 raxmlHPC-PTHREADS-AVX $PKG/usr/bin/raxmlHPC-PTHREADS-AVX + +## Default coarse-grain MPI version +#make -f Makefile.MPI.gcc +#install -D -m755 raxmlHPC-MPI $PKG/usr/bin/raxmlHPC-MPI + +#make -f Makefile.SSE3.MPI.gcc +#install -D -m755 raxmlHPC-MPI-SSE3 $PKG/usr/bin/raxmlHPC-MPI-SSE3 + +#make -f Makefile.AVX.MPI.gcc +#install -D -m755 raxmlHPC-MPI-AVX $PKG/usr/bin/raxmlHPC-MPI-AVX + +## Hybrid MPI/Pthreads version +# Before using this version, please read this paper here: +# http://sco.h-its.org/exelixis/pubs/Exelixis-RRDR-2010-3.pdf +# and look at these slides: +# http://sco.h-its.org/exelixis/resource/doc/Phylo100225.pdf +#make -f Makefile.HYBRID.gcc +#install -D -m755 raxmlHPC-HYBRID $PKG/usr/bin/raxmlHPC-HYBRID + +#make -f Makefile.SSE3.HYBRID.gcc +#install -D -m755 raxmlHPC-HYBRID-SSE3 $PKG/usr/bin/raxmlHPC-HYBRID-SSE3 + +#make -f Makefile.AVX.HYBRID.gcc +#install -D -m755 raxmlHPC-HYBRID-AVX $PKG/usr/bin/raxmlHPC-HYBRID-AVX + +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 + +# Copy the useful scripts +mkdir -p $PKG/usr/share/$PRGNAM +cp -a usefulScripts $PKG/usr/share/$PRGNAM + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a README manual $PKG/usr/doc/$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/RAxML/RAxML.info b/academic/RAxML/RAxML.info new file mode 100644 index 0000000000..a6ef346e17 --- /dev/null +++ b/academic/RAxML/RAxML.info @@ -0,0 +1,10 @@ +PRGNAM="RAxML" +VERSION="8.2.12" +HOMEPAGE="https://cme.h-its.org/exelixis/web/software/raxml/index.html" +DOWNLOAD="https://github.com/stamatak/standard-RAxML/archive/v8.2.12/standard-RAxML-8.2.12.tar.gz" +MD5SUM="4ac68b0156bc52fe056207ba8ef719d2" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="openmpi" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/RAxML/README b/academic/RAxML/README new file mode 100644 index 0000000000..b03ec92b2e --- /dev/null +++ b/academic/RAxML/README @@ -0,0 +1,16 @@ +RAxML - Randomized Axelerated Maximum Likelihood + +RAxML is a program for sequential and parallel Maximum Likelihood (ML) +based inference of large phylogenetic trees. It can also be used for +postanalyses of sets of phylogenetic trees, analyses of alignments and, +evolutionary placement of short reads. + +NOTE! +The script builds single threaded and mpi versions of the executable +with Slackware's default compiler flags. You are highly encouraged to +check the script for building with other flags and optimisations. This +will dramatically speed up RAxML on modern processors. + +When using RAxML please cite the following paper: A. Stamatakis: +"RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of +Large Phylogenies". In Bioinformatics, 2014 diff --git a/academic/RAxML/References b/academic/RAxML/References new file mode 100644 index 0000000000..971db2e337 --- /dev/null +++ b/academic/RAxML/References @@ -0,0 +1,4 @@ +When using RAxML please cite the following paper: A. Stamatakis: +"RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of +Large Phylogenies". In Bioinformatics, 2014, open access. + diff --git a/academic/RAxML/slack-desc b/academic/RAxML/slack-desc new file mode 100644 index 0000000000..7dbc6b8967 --- /dev/null +++ b/academic/RAxML/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------------------------------------------------------| +RAxML: RAxML (Randomized Axelerated Maximum Likelihood) +RAxML: +RAxML: RAxML is a program for sequential and parallel Maximum Likelihood +RAxML: (ML) based inference of large phylogenetic trees. It can also be +RAxML: used for postanalyses of sets of phylogenetic trees, analyses of +RAxML: alignments and, evolutionary placement of short reads. +RAxML: +RAxML: https://cme.h-its.org/exelixis/web/software/raxml/index.html +RAxML: https://github.com/stamatak/standard-RAxML +RAxML: +RAxML: -- cgit v1.2.3