From b9ec7b5ad1a16a2ad3eef68344959950091ff7c7 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Fri, 21 Apr 2023 01:57:50 +0100 Subject: [PATCH] academic/treerecs: Added (Treerecs: a tree reconciliation tool) Signed-off-by: bedlam Signed-off-by: Willy Sudiarto Raharjo --- academic/treerecs/README | 38 ++++++++ academic/treerecs/doinst.sh | 3 + academic/treerecs/slack-desc | 19 ++++ academic/treerecs/treerecs.SlackBuild | 123 ++++++++++++++++++++++++++ academic/treerecs/treerecs.info | 10 +++ 5 files changed, 193 insertions(+) create mode 100644 academic/treerecs/README create mode 100644 academic/treerecs/doinst.sh create mode 100644 academic/treerecs/slack-desc create mode 100644 academic/treerecs/treerecs.SlackBuild create mode 100644 academic/treerecs/treerecs.info diff --git a/academic/treerecs/README b/academic/treerecs/README new file mode 100644 index 0000000000..283164480a --- /dev/null +++ b/academic/treerecs/README @@ -0,0 +1,38 @@ +Treerecs: a tree reconciliation tool + +Treerecs is an open-source (species- and gene-) tree reconciliation +software distributed under the GNU AGPL licence. It can correct, +rearrange and (re-)root gene trees with regard to a given species tree. +It was designed to be both efficient and easy to install and to use. + +Features +- Correct gene trees with regard to a reference species tree +- Root or re-root gene trees +- Contract gene-tree branches whose support is lower than a given + threshold, thus creating polytomies (multifurcations) that can be + resolved therefater +- Sample solutions with equivalent scores +- Produce a graphical representation of the reconciled trees +- Supported formats + +Treerecs supports the following formats: Newick, NHX, PhyloXML, +recPhyloXML, SVG (graphical output). + +A program that can drive Treerecs, providing a GUI is Seaview, also +available at SBo. The SlacBuild script builds two additional programs: + +1) ALEevaluate_undated: an executable of the ALE (Amalgamated likelihood +estimation, https://github.com/ssolo/ALE), by Szollosi GJ et al). This +version has other mapping options and a different implementation in +Bio++ use. + +2) genetreeEditor: a small program which provides editing of gene names +using species names and format conversion (Newick, Nhx or PhyloXML) . + +For more information, see preprint at bioRxiv: +Treerecs: an integrated phylogenetic tool, from sequences to +reconciliations. Nicolas Comte, Benoit Morel, Damir Hasic, Laurent +Guéguen, Bastien Boussau, Vincent Daubin, Simon Penel, Celine +Scornavacca, Manolo Gouy, Alexandros Stamatakis, Eric Tannier. +View ORCID ProfileDavid P. Parsons +https://www.biorxiv.org/content/10.1101/782946v1 diff --git a/academic/treerecs/doinst.sh b/academic/treerecs/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/treerecs/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi diff --git a/academic/treerecs/slack-desc b/academic/treerecs/slack-desc new file mode 100644 index 0000000000..319b6b6f7b --- /dev/null +++ b/academic/treerecs/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------------------------------------------------------| +treerecs: treerecs (Treerecs: a tree reconciliation tool) +treerecs: +treerecs: Treerecs is an open-source (species- and gene-) tree reconciliation +treerecs: software. It can correct, rearrange and (re-)root gene trees with +treerecs: regard to a given species tree. +treerecs: +treerecs: https://project.inria.fr/treerecs/ +treerecs: https://gitlab.inria.fr/Phylophile/Treerecs +treerecs: +treerecs: +treerecs: diff --git a/academic/treerecs/treerecs.SlackBuild b/academic/treerecs/treerecs.SlackBuild new file mode 100644 index 0000000000..14e1cebfe0 --- /dev/null +++ b/academic/treerecs/treerecs.SlackBuild @@ -0,0 +1,123 @@ +#!/bin/bash + +# Slackware build script for treerecs + +# Copyright 2020-2023 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. + +# Thanks to David Parsons for clarifications about the scipt and suggestions! + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=treerecs +SRCNAM=Treerecs +VERSION=${VERSION:-1.2} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +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 $SRCNAM-v${VERSION} +tar xvf $CWD/$SRCNAM-v${VERSION}.tar.gz +cd $SRCNAM-v${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 {} \; + +# GCC 12 explicitly requires these +# https://stackoverflow.com/a/68149587 +sed -i "45i #include " ext/bpp/bpp-core/src/Bpp/Graph/GlobalGraph.cpp +sed -i "26i #include " src/treerecs/containers/AbstractGrid.h + +mkdir -p build +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_BUILD_TYPE=Release .. + make +cd .. + +# This is the program executable. Using "make install DESTDIR=$PKG" +# works, but it simply puts treerecs in /usr/local/bin and that's it +install -D -m755 build/bin/$PRGNAM $PKG/usr/bin/$PRGNAM + +# Include the extra binaries +install -D -m755 build/bin/misc/ALEevaluate_undated $PKG/usr/bin/ALEevaluate_undated +install -D -m755 build/bin/misc/genetreeEditor $PKG/usr/bin/genetreeEditor + +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 some examples and the icon just in case +mkdir -p $PKG/usr/share/$PRGNAM +cp -a examples ${PRGNAM}_icon.png $PKG/usr/share/$PRGNAM + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + AUTHORS COPYING CONTRIBUTING.md README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +cp -a build/bin/misc/README.md $PKG/usr/doc/$PRGNAM-$VERSION/README-misc.md +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/treerecs/treerecs.info b/academic/treerecs/treerecs.info new file mode 100644 index 0000000000..f6a81aa05b --- /dev/null +++ b/academic/treerecs/treerecs.info @@ -0,0 +1,10 @@ +PRGNAM="treerecs" +VERSION="1.2" +HOMEPAGE="https://project.inria.fr/treerecs/" +DOWNLOAD="https://gitlab.inria.fr/Phylophile/Treerecs/-/archive/v1.2/Treerecs-v1.2.tar.gz" +MD5SUM="a85d2dc0047278bfb0017c2b69824b56" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com"