academic/treerecs: Removed (ftb + no active maintainer).

Signed-off-by: Matteo Bernardini <ponce@slackbuilds.org>

5 files changed, 0 insertions, 191 deletions

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"