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| -rw-r--r-- | academic/paml/LICENSE | 3 | ||||
| -rw-r--r-- | academic/paml/README | 18 | ||||
| -rw-r--r-- | academic/paml/References | 6 | ||||
| -rw-r--r-- | academic/paml/paml.SlackBuild | 158 | ||||
| -rw-r--r-- | academic/paml/paml.info | 10 | ||||
| -rw-r--r-- | academic/paml/slack-desc | 19 |
6 files changed, 214 insertions, 0 deletions
diff --git a/academic/paml/LICENSE b/academic/paml/LICENSE new file mode 100644 index 0000000000000..b58e2508621b4 --- /dev/null +++ b/academic/paml/LICENSE @@ -0,0 +1,3 @@ +PAML is maintained and distributed for academic use free of charge by +Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac +OSX, and executables are provided for MS Windows. diff --git a/academic/paml/README b/academic/paml/README new file mode 100644 index 0000000000000..5703a8d4d07fc --- /dev/null +++ b/academic/paml/README @@ -0,0 +1,18 @@ +PAML: Phylogenetic Analysis by Maximum Likelihood + +PAML is a package of programs for phylogenetic analyses of DNA or +protein sequences using maximum likelihood. PAML is not good for tree +making. It may be used to estimate parameters and test hypotheses to +study the evolutionary process, when you have reconstructed trees +using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc. + +Notes about running of PAML programs and the package: + +- Example datasets are included in /usr/share/paml/examples +- Control files for PAML programs are in /usr/share/paml +- Dcumentation can be found in /usr/doc/paml-$VERSION +- Additional executables are placed in /usr/libexec/paml + +Suggested citation: +Yang, Z. 2007. PAML 4: a program package for phylogenetic analysis by +maximum likelihood. Molecular Biology and Evolution 24: 1586-1591 diff --git a/academic/paml/References b/academic/paml/References new file mode 100644 index 0000000000000..edc41e24aa9e8 --- /dev/null +++ b/academic/paml/References @@ -0,0 +1,6 @@ +Suggested citations: +Yang, Z. 1997. PAML: a program package for phylogenetic analysis by +maximum likelihood Computer Applications in BioSciences 13:555-556. +Yang, Z. 2007. PAML 4: a program package for phylogenetic analysis by +maximum likelihood. Molecular Biology and Evolution 24: 1586-1591 +(http://abacus.gene.ucl.ac.uk/software/paml.html). diff --git a/academic/paml/paml.SlackBuild b/academic/paml/paml.SlackBuild new file mode 100644 index 0000000000000..ab866fd536028 --- /dev/null +++ b/academic/paml/paml.SlackBuild @@ -0,0 +1,158 @@ +#!/bin/sh + +# Slackware build script for paml + +# Copyright 2013 Petar Petrov, petar.petrov@student.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=paml +VERSION=${VERSION:-4.7a} +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}.tgz +cd ${PRGNAM}${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 {} \; + +# Use our CFLAGS +sed -i "/^C.*.*FLAGS/s/=/+=/" src/Makefile + +# These are the main components, and most likely this will be all you +# need. Check the next sections if you need some optional components. +# They will be installed to /usr/libexec/paml in case you want them. +cd src +CFLAGS="$SLKCFLAGS" \ +make -f Makefile + +install -D -m755 baseml $PKG/usr/bin/baseml +install -D -m755 basemlg $PKG/usr/bin/basemlg +install -D -m755 chi2 $PKG/usr/bin/chi2 +install -D -m755 codeml $PKG/usr/bin/codeml +install -D -m755 evolver $PKG/usr/bin/evolver +install -D -m755 mcmctree $PKG/usr/bin/mcmctree +install -D -m755 pamp $PKG/usr/bin/pamp +install -D -m755 yn00 $PKG/usr/bin/yn00 + +# Compile and install Evolver variations +cc $SLKCFLAGS -DCodonNSbranches -o evolverNSbranches evolver.c tools.c -lm +cc $SLKCFLAGS -DCodonNSsites -o evolverNSsites evolver.c tools.c -lm +cc $SLKCFLAGS -DCodonNSbranchsites -o evolverNSbranchsites evolver.c tools.c -lm + +install -D -m755 evolverNSbranches $PKG/usr/libexec/$PRGNAM/evolverNSbranches +install -D -m755 evolverNSbranchsites $PKG/usr/libexec/$PRGNAM/evolverNSbranchsites +install -D -m755 evolverNSsites $PKG/usr/libexec/$PRGNAM/evolverNSsites + +# Compile and install TreeTime +cc $SLKCFLAGS -o TreeTimeJeff TreeTimeJeff.c tools.c -lm +install -D -m755 TreeTimeJeff $PKG/usr/libexec/$PRGNAM/TreeTimeJeff + +# Rename the local README, so we include it in the package. +mv README.txt README-compiling.txt + +# Compile and install NEB, BEB and BranchSite +cd ../Technical/Simulation/Codon +cc $SLKCFLAGS -DNEB -o PositiveSitesNEB PositiveSites.c -lm +cc $SLKCFLAGS -DBEB -o PositiveSitesBEB PositiveSites.c -lm +cc $SLKCFLAGS -DBranchSite -o PositiveSitesBS PositiveSites.c -lm + +install -D -m755 PositiveSitesBEB $PKG/usr/libexec/$PRGNAM/PositiveSitesBEB +install -D -m755 PositiveSitesBS $PKG/usr/libexec/$PRGNAM/PositiveSitesBS +install -D -m755 PositiveSitesNEB $PKG/usr/libexec/$PRGNAM/PositiveSitesNEB + +# Rename this README too so we include it in the package. +mv README.txt README-codon.txt + +# Compile and install Multiruns +cd .. +cc -o multiruns $SLKCFLAGS multiruns.c -lm +install -D -m755 multiruns $PKG/usr/libexec/$PRGNAM/multiruns + +cd $TMP/${PRGNAM}${VERSION} + +# Include sample system files and example experimental data. +mkdir -p $PKG/usr/share/$PRGNAM/{aa,codon,ctl,dat,nuc,paup,trees} +cp -a *.dat dat/* $PKG/usr/share/$PRGNAM/dat +cp -a Technical/Simulation/Codon/{codeml.ctl,*.dat} \ + $PKG/usr/share/$PRGNAM/codon +cp -a examples $PKG/usr/share/$PRGNAM +cp -a *.aa $PKG/usr/share/$PRGNAM/aa +cp -a *.ctl $PKG/usr/share/$PRGNAM/ctl +cp -a *.nuc $PKG/usr/share/$PRGNAM/nuc +cp -a paup* $PKG/usr/share/$PRGNAM/paup +cp -a *.trees $PKG/usr/share/$PRGNAM/trees + +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 \ + README.txt GeneticCode.txt doc/* src/README-compiling.txt \ + Technical/{Pt/eigenQREV.pdf,Simulation/{multiruns.txt,Codon/README-codon.txt}}\ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/LICENSE > $PKG/usr/doc/$PRGNAM-$VERSION/LICENSE + +# Fix permissions. +find $PKG/usr/{doc,share} -type d -exec chmod 755 {} \; -o \ + -type f -exec chmod 644 {} \; + +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/paml/paml.info b/academic/paml/paml.info new file mode 100644 index 0000000000000..653abc36094c9 --- /dev/null +++ b/academic/paml/paml.info @@ -0,0 +1,10 @@ +PRGNAM="paml" +VERSION="4.7a" +HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html" +DOWNLOAD="http://abacus.gene.ucl.ac.uk/software/paml4.7a.tgz" +MD5SUM="59b330e6ba15b1e79a02ff3817b96346" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="petar.petrov@student.oulu.fi" diff --git a/academic/paml/slack-desc b/academic/paml/slack-desc new file mode 100644 index 0000000000000..86ae56d94fddf --- /dev/null +++ b/academic/paml/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------------------------------------------------------| +paml: paml (PAML: Phylogenetic Analysis by Maximum Likelihood) +paml: +paml: PAML is a package of programs for phylogenetic analyses of DNA or +paml: protein sequences using maximum likelihood. PAML is not good for +paml: tree making. It may be used to estimate parameters and test +paml: hypotheses to study the evolutionary process, when you have +paml: reconstructed trees using other programs such as PAUP*, PHYLIP, +paml: MOLPHY, PhyML, RaxML, etc. +paml: +paml: Home: http://abacus.gene.ucl.ac.uk/software/paml.html +paml: References: /usr/doc/paml-4.7a/References |