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academic/treerecs: Added (Treerecs: a tree reconciliation tool)
Signed-off-by: bedlam <dave@slackbuilds.org> Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Petar Petrov
Willy Sudiarto Raharjo
parent
942e26bee8
commit
b9ec7b5ad1
5 changed files with 193 additions and 0 deletions
38
academic/treerecs/README
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38
academic/treerecs/README
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Treerecs: a tree reconciliation tool
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Treerecs is an open-source (species- and gene-) tree reconciliation
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software distributed under the GNU AGPL licence. It can correct,
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rearrange and (re-)root gene trees with regard to a given species tree.
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It was designed to be both efficient and easy to install and to use.
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Features
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- Correct gene trees with regard to a reference species tree
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- Root or re-root gene trees
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- Contract gene-tree branches whose support is lower than a given
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threshold, thus creating polytomies (multifurcations) that can be
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resolved therefater
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- Sample solutions with equivalent scores
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- Produce a graphical representation of the reconciled trees
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- Supported formats
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Treerecs supports the following formats: Newick, NHX, PhyloXML,
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recPhyloXML, SVG (graphical output).
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A program that can drive Treerecs, providing a GUI is Seaview, also
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available at SBo. The SlacBuild script builds two additional programs:
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1) ALEevaluate_undated: an executable of the ALE (Amalgamated likelihood
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estimation, https://github.com/ssolo/ALE), by Szollosi GJ et al). This
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version has other mapping options and a different implementation in
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Bio++ use.
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2) genetreeEditor: a small program which provides editing of gene names
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using species names and format conversion (Newick, Nhx or PhyloXML) .
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For more information, see preprint at bioRxiv:
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Treerecs: an integrated phylogenetic tool, from sequences to
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reconciliations. Nicolas Comte, Benoit Morel, Damir Hasic, Laurent
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Guéguen, Bastien Boussau, Vincent Daubin, Simon Penel, Celine
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Scornavacca, Manolo Gouy, Alexandros Stamatakis, Eric Tannier.
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View ORCID ProfileDavid P. Parsons
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https://www.biorxiv.org/content/10.1101/782946v1
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3
academic/treerecs/doinst.sh
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3
academic/treerecs/doinst.sh
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if [ -x /usr/bin/update-desktop-database ]; then
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/usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1
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fi
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19
academic/treerecs/slack-desc
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19
academic/treerecs/slack-desc
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# HOW TO EDIT THIS FILE:
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# The "handy ruler" below makes it easier to edit a package description.
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# Line up the first '|' above the ':' following the base package name, and
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# the '|' on the right side marks the last column you can put a character in.
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# You must make exactly 11 lines for the formatting to be correct. It's also
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# customary to leave one space after the ':' except on otherwise blank lines.
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|-----handy-ruler------------------------------------------------------|
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treerecs: treerecs (Treerecs: a tree reconciliation tool)
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treerecs:
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treerecs: Treerecs is an open-source (species- and gene-) tree reconciliation
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treerecs: software. It can correct, rearrange and (re-)root gene trees with
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treerecs: regard to a given species tree.
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treerecs:
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treerecs: https://project.inria.fr/treerecs/
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treerecs: https://gitlab.inria.fr/Phylophile/Treerecs
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treerecs:
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treerecs:
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treerecs:
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123
academic/treerecs/treerecs.SlackBuild
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123
academic/treerecs/treerecs.SlackBuild
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#!/bin/bash
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# Slackware build script for treerecs
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# Copyright 2020-2023 Petar Petrov slackalaxy@gmail.com
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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# permitted provided that the following conditions are met:
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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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# Thanks to David Parsons for clarifications about the scipt and suggestions!
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cd $(dirname $0) ; CWD=$(pwd)
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PRGNAM=treerecs
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SRCNAM=Treerecs
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VERSION=${VERSION:-1.2}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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PKGTYPE=${PKGTYPE:-tgz}
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i586 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( uname -m ) ;;
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esac
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fi
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if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then
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echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE"
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exit 0
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fi
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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if [ "$ARCH" = "i586" ]; then
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SLKCFLAGS="-O2 -march=i586 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "i686" ]; then
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SLKCFLAGS="-O2 -march=i686 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "x86_64" ]; then
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SLKCFLAGS="-O2 -fPIC"
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LIBDIRSUFFIX="64"
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else
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SLKCFLAGS="-O2"
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LIBDIRSUFFIX=""
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fi
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set -e
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf $SRCNAM-v${VERSION}
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tar xvf $CWD/$SRCNAM-v${VERSION}.tar.gz
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cd $SRCNAM-v${VERSION}
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chown -R root:root .
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find -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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-o -perm 511 \) -exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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# GCC 12 explicitly requires these
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# https://stackoverflow.com/a/68149587
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sed -i "45i #include <limits>" ext/bpp/bpp-core/src/Bpp/Graph/GlobalGraph.cpp
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sed -i "26i #include <utility>" src/treerecs/containers/AbstractGrid.h
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mkdir -p build
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cd build
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cmake \
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-DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \
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-DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \
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-DCMAKE_BUILD_TYPE=Release ..
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make
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cd ..
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# This is the program executable. Using "make install DESTDIR=$PKG"
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# works, but it simply puts treerecs in /usr/local/bin and that's it
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install -D -m755 build/bin/$PRGNAM $PKG/usr/bin/$PRGNAM
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# Include the extra binaries
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install -D -m755 build/bin/misc/ALEevaluate_undated $PKG/usr/bin/ALEevaluate_undated
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install -D -m755 build/bin/misc/genetreeEditor $PKG/usr/bin/genetreeEditor
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find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
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| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
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# Copy some examples and the icon just in case
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mkdir -p $PKG/usr/share/$PRGNAM
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cp -a examples ${PRGNAM}_icon.png $PKG/usr/share/$PRGNAM
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a \
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AUTHORS COPYING CONTRIBUTING.md README.md \
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$PKG/usr/doc/$PRGNAM-$VERSION
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cp -a build/bin/misc/README.md $PKG/usr/doc/$PRGNAM-$VERSION/README-misc.md
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cat $CWD/doinst.sh > $PKG/install/doinst.sh
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE
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10
academic/treerecs/treerecs.info
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10
academic/treerecs/treerecs.info
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PRGNAM="treerecs"
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VERSION="1.2"
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HOMEPAGE="https://project.inria.fr/treerecs/"
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DOWNLOAD="https://gitlab.inria.fr/Phylophile/Treerecs/-/archive/v1.2/Treerecs-v1.2.tar.gz"
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MD5SUM="a85d2dc0047278bfb0017c2b69824b56"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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REQUIRES=""
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MAINTAINER="Petar Petrov"
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EMAIL="slackalaxy@gmail.com"
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