From 30062d8496b821d13c594671a18f456bf34108b9 Mon Sep 17 00:00:00 2001 From: Matteo Bernardini Date: Sun, 27 Feb 2022 21:09:29 +0100 Subject: academic/treerecs: Removed (ftb + no active maintainer). Signed-off-by: Matteo Bernardini --- academic/treerecs/README | 37 ----------- academic/treerecs/doinst.sh | 3 - academic/treerecs/slack-desc | 19 ------ academic/treerecs/treerecs.SlackBuild | 122 ---------------------------------- academic/treerecs/treerecs.info | 10 --- 5 files changed, 191 deletions(-) delete mode 100644 academic/treerecs/README delete mode 100644 academic/treerecs/doinst.sh delete mode 100644 academic/treerecs/slack-desc delete mode 100644 academic/treerecs/treerecs.SlackBuild delete mode 100644 academic/treerecs/treerecs.info (limited to 'academic/treerecs') diff --git a/academic/treerecs/README b/academic/treerecs/README deleted file mode 100644 index e338496bfb..0000000000 --- a/academic/treerecs/README +++ /dev/null @@ -1,37 +0,0 @@ -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 deleted file mode 100644 index 5fb28930db..0000000000 --- a/academic/treerecs/doinst.sh +++ /dev/null @@ -1,3 +0,0 @@ -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 deleted file mode 100644 index 319b6b6f7b..0000000000 --- a/academic/treerecs/slack-desc +++ /dev/null @@ -1,19 +0,0 @@ -# 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 deleted file mode 100644 index abaf7ba814..0000000000 --- a/academic/treerecs/treerecs.SlackBuild +++ /dev/null @@ -1,122 +0,0 @@ -#!/bin/bash - -# Slackware build script for treerecs - -# Copyright 2020-2021 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 -VERSION=${VERSION:-1.2} -BUILD=${BUILD:-1} -TAG=${TAG:-_SBo} -PKGTYPE=${PKGTYPE:-tgz} - -SRCNAM=Treerecs - -if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i586 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac -fi - -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. -if [ ! -z "${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 {} \; - -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 deleted file mode 100644 index f6a81aa05b..0000000000 --- a/academic/treerecs/treerecs.info +++ /dev/null @@ -1,10 +0,0 @@ -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" -- cgit v1.2.3-65-gdbad